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@INPROCEEDINGS{blow-etal-88,
  author = { D. M. Blow and K. Henrick and A. Vrielink},
  title = {Practical Problems of Isomorphous Replacement},
  pages = {32--38},
  crossref = {study-w/e-88},
}

@INPROCEEDINGS{bricogne-91,
  author = {G. Bricogne},
  title = {A maximum-likelihood theory of heavy-atom parameter
	
	  refinement in the isomorphous replacement method},
  pages = {60--68},
  crossref = {study-w/e-91},
}

@ARTICLE{prolsq,
  author = {W. Hendrickson},
  title = {Practical aspects of stereochemically restrained
	
	  refinement of protein structures},
  pages = {1--12},
  crossref = {study-w/e-80},
  optnote = {prolsq},
}

@INCOLLECTION{lamzin/wilson-92,
  author = {Victor S. Lamzin and Keith S. Wilson},
  title = {Automated Refinement Procedure},
  pages = {76},
  crossref = {study-w/e-92},
  optnote = {ARP},
}

@INCOLLECTION{lattman-85,
  author = {Lattman, E. E},
  title = {Use of the Rotation and Translation Functions},
  pages = {55--76},
  crossref = {wyckoff-85b},
}

@INPROCEEDINGS{leslie-88,
  author = {A. G. W. Leslie},
  title = {A Reciprocal Space Algorithm for Calculating
	
	  Molecular Envelope using the Algorithm of {B. C. Wang}},
  pages = {25--31},
  crossref = {study-w/e-88},
}

@ARTICLE{murray-rust/zelinka-93,
  author = {Peter Murray-Rust and Jan Zelinka},
  title = {New Approaches to Crystallographic Software},
  pages = {212--231},
  crossref = {cc6},
  optannote = {original zldb},
  optnote = {See also \texttt{http:/\slash
	
	  www.yorvic.york.ac.uk\slash \~zelinka}.},
}

@INPROCEEDINGS{denzo,
  author = {Zbyszek Otwinowski},
  title = {Oscillation data reduction program},
  pages = {56},
  crossref = {study-w/e-93},
  optnote = {denzo},
}

@INPROCEEDINGS{otwinowski-91,
  author = {Zbyszek Otwinowski},
  title = {Maximum likelihood refinement of heavy atom parameters},
  pages = {80},
  crossref = {study-w/e-91},
  optnote = {mlphare},
}

@INPROCEEDINGS{priestle-95,
  author = {J. P. Priestle},
  title = {Consistent Stereochemical Dictionaries for Refinement and Model Building},
  pages = {25--32},
  crossref = {study-w/e-95},
}

@INPROCEEDINGS{read-91,
  author = {R. J. Read},
  title = {Dealing with imperfect isomorphism in multiple
	
	  isomorphous replacement},
  pages = {69--79},
  crossref = {study-w/e-91},
}

@INCOLLECTION{richards-85,
  author = {Frederic M. Richards},
  title = {Calculation of Molecular Volumes and Areas for
	
	  Structures of Known Geometry},
  pages = {440--464},
  crossref = {wyckoff-85b},
  optnote = {SURFACE/VOLUME},
}

@INCOLLECTION{richardson-85,
  author = {Jane S. Richardson},
  title = {Schematic Drawings of Protein Structures},
  pages = {359--380},
  crossref = {wyckoff-85b},
  optnote = {ribbon diagrams},
}

@INPROCEEDINGS{sheldrick-91,
  author = {G. M. Sheldrick},
  title = {Heavy atom location using SHELXS-90},
  pages = {23--38},
  crossref = {study-w/e-91},
}

@INPROCEEDINGS{sheldrick-92,
  author = {G. M. Sheldrick},
  pages = {145--157},
  crossref = {cc5},
  optnote = {SHELXS-90 Pattersons},
}

@ARTICLE{corels,
  author = {Joel L. Sussman},
  title = {Use of {CORELS} for the refinement of biological
	
	  macromolecules},
  pages = {13--23},
  crossref = {study-w/e-80},
  optnote = {corels},
}

@INCOLLECTION{teneyck-85,
  author = {Ten Eyck, L. F.},
  title = {Fast Fourier Transform Calculation of Electron
	
	  Density Maps},
  pages = {324--340},
  crossref = {wyckoff-85b},
}

@INPROCEEDINGS{tickle-85,
  author = {I. J. Tickle},
  title = {Review of space group general translation functions
	
	  that make use of known structure information and can be expanded
	as
	
	  {F}ourier series},
  pages = {22--26},
  crossref = {study-w/e-85},
}

@INPROCEEDINGS{tickle-92,
  author = {I. J. Tickle},
  title = {Fast {F}ourier Translation Functions},
  pages = {20--32},
  crossref = {study-w/e-92},
}

@INPROCEEDINGS{tickle-91,
  author = {Ian Tickle},
  title = {Refinement of SIR heavy atom parameters in Patterson vs
	
	 reciprocal space},
  pages = {87-95},
  crossref = {study-w/e-91},
  optnote = {fhscal, vecref},
}

@INPROCEEDINGS{tronrud-94,
  author = {D. E. Tronrud},
  title = {Methods of Minimization and their Implications},
  pages = {111--124},
  crossref = {study-w/e-94},
}

@INCOLLECTION{wang-85,
  author = {Bi-Cheng Wang},
  title = {Resolution of Phase Ambiguity in Macromolecular
	
	  Crystallography},
  pages = {90--113},
  crossref = {wyckoff-85b},
}

@MISC{merritt-95,
  author = {Ethan A.~Merritt},
  title = {X-ray Anomalous Scattering},
  howpublished = {{}\texttt{http:/\slash brie.bmsc.washington.edu:80\slash scatter/}},
  year = {1995},
}

@ARTICLE{adams:97,
  author = {Adams, P. D. and Pannu, N. S. and Read, R. J. and Brunger, A. T.},
  title = {Cross-validated maximum likelihood enhances
 crystallographic simulated
	annealing refinement},
  journal = {PNAS},
  year = {1997},
  volume = {94},
  pages = {5018-5023},
  number = {10},
}

@ARTICLE{agarwal-78,
  author = {R. C. Agarwal},
  title = {A new Least-Squares Refinement Technique based on
	
	  the Fast {Fourier} Transform},
  journal = ac,
  year = {1978},
  volume = {A34},
  pages = {791--809},
  optnote = {sfall},
}

@ARTICLE{baker-etal-94,
  author = {Baker, D. and Bystroff, C. and Fletterick, R. J. and Agard,
	
	    D. A.},
  journal = ac,
  year = {1994},
  volume = {D49},
  optnote = {PRISM},
}

@ARTICLE{Barton1993,
  author = {GJ Barton},
  title = {A{LSCRIPT}: a tool to format multiple sequence alignments.},
  journal = {Protein Eng},
  year = {1993},
  volume = {6},
  pages = {37-40},
  number = {1},
  month = {Jan},
  keywords = {Amino Acid Sequence, Annexins, Data Display, Molecular Sequence Data,
	Printing, Protein Structure, Secondary, Sequence Alignment, Sequence
	Homology, Amino Acid, 8433969},
  owner = {brooks},
}

@ARTICLE{berman:00,
  author = {Berman, H. M. and Westbrook, J. and Feng, Z. and
 Gilliland, G. and
	Bhat, T. N. and Weissig, H. and
 Shindyalov, I. N. and Bourne, P.
	E.},
  title = {The Protein Data Bank},
  journal = {Nucleic Acids Res.},
  year = {2000},
  volume = {28},
  pages = {235-242},
  number = {1},
}

@ARTICLE{Bhat1988,
  author = {Bhat, T. N.},
  title = {{Calculation of an OMIT map}},
  journal = {Journal of Applied Crystallography},
  year = {1988},
  volume = {21},
  pages = {279--281},
  number = {3},
  month = {Jun},
  pdf = {Bhat_Calculation_of_an_OMIT_map.pdf},
}

@ARTICLE{blow-58,
  author = {D. M. Blow},
  journal = {Proc. Roy. Soc.},
  year = {1958},
  volume = {A247},
  pages = {302},
}

@ARTICLE{blow/crick-59,
  author = {D. M. Blow and F. H. C. Crick},
  journal = ac,
  year = {1959},
  volume = {12},
  pages = {794--802},
}

@ARTICLE{blow/matthews-73,
  author = {D. M. Blow and B. W. Matthews},
  journal = ac,
  year = {1973},
  volume = {A29},
  pages = {56--62},
}

@ARTICLE{blow/rossmann-61,
  author = {D. M. Blow and M. G. Rossmann},
  title = {The Single Isomorphous Replacement Method},
  journal = ac,
  year = {1961},
  volume = {14},
  pages = {1195--1202},
}

@BOOK{blundell/johnson,
  title = {Protein Crystallography},
  publisher = {Academic Press},
  year = {1976},
  author = {T. L. Blundell and L. N. Johnson},
  address = {London},
}

@BOOK{bracewell-78,
  title = {The Fourier Transformation and its Applications},
  publisher = {Mc.~Graw-Hill},
  year = {1978},
  author = {R. N. Bracewell},
  edition = {Second},
  optnote = {ISBN 0--07--Y66454--4},
}

@ARTICLE{branden/jones,
  author = {C. Branden and A. Jones},
  title = {Between Objectivity and Subjectivity},
  journal = {Nature},
  year = {1990},
  volume = {343},
  pages = {687--689},
  optnote = {overlapmap (real space R-factor)},
}

@INPROCEEDINGS{bricogne-82,
  author = { G. Bricogne },
  booktitle = {Computational Crystallography},
  year = {1982},
  editor = {D. Sayre},
  pages = {223--230},
  address = {Oxford},
  publisher = {Clarendon Press},
}

@ARTICLE{bricogne-76,
  author = {Bricogne, G.},
  title = {Methods and Programs for Direct-Space Exploitation
	
	  of Geometric Redundancies},
  journal = ac,
  year = {1976},
  volume = {A32},
  pages = {832-847},
}

@ARTICLE{bricogne-74,
  author = {Bricogne, G.},
  title = {Geometric Sources of Redundancy in Intensity Data
	
	  and Their Use for Phase Determination},
  journal = ac,
  year = {1974},
  volume = {A30},
  pages = {395--405},
  optnote = {NCS averaging},
}

@ARTICLE{brunger:98,
  author = {Brunger, A. T. and Adams, P. D. and Clore, G. M. and
 DeLano, W.
	L. and Gros, P. and Grosse-Kunstleve,
 R. W. and Jiang, J. S. and
	Kuszewski, J. and Nilges,
 M. and Pannu, N. S. and Read, R. J. and
	Rice,
 L. M. and Simonson, T. and Warren, G. L.},
  title = {Crystallography \& {NMR} system: A new software suite for
 macromolecular
	structure determination},
  journal = {Acta Cryst.},
  year = {1998},
  volume = {D54},
  pages = {905-921},
}

@ARTICLE{brunger:92,
  author = {Brunger, A.T.},
  title = {The free {R} value: a novel statistical quantity for
 assessing the
	accuracy of crystal structures},
  journal = {Nature},
  year = {1992},
  volume = {355},
  pages = {472-474},
}

@ARTICLE{brunger-92,
  author = {A. T. Br{\"u}nger},
  title = {The Free {$R$} value: a Novel Statistical Quantity
	
	  for Assessing the Accuracy of Crystal Structures},
  journal = {Nature},
  year = {1992},
  volume = {355},
  pages = {472--474},
  optnote = {freerflag, sfall},
}

@ARTICLE{Burmeister2000,
  author = {WP Burmeister},
  title = {Structural changes in a cryo-cooled protein crystal owing to radiation
	damage.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {2000},
  volume = {56 ( Pt 3)},
  pages = {328-41},
  month = {Mar},
  abstract = {The high intensity of third-generation X-ray sources, along with the
	development of cryo-cooling of protein crystals at temperatures around
	100 K, have made it possible to extend the diffraction limit of crystals
	and to reduce their size. However, even with cryo-cooled crystals,
	radiation damage becomes a limiting factor. So far, the radiation
	damage has manifested itself in the form of a loss of overall diffracted
	intensity and an increase in the temperature factor. The structure
	of a protein (myrosinase) after exposure to different doses of X-rays
	in the region of 20 x 10(15) photons mm(-2) has been studied. The
	changes in the structure owing to radiation damage were analysed
	using Fourier difference maps and occupancy refinement for the first
	time. Damage was obvious in the form of breakage of disulfide bonds,
	decarboxylation of aspartate and glutamate residues, a loss of hydroxyl
	groups from tyrosine and of the methylthio group of methionine. The
	susceptibility to radiation damage of individual groups of the same
	kind varies within the protein. The quality of the model resulting
	from structure determination might be compromised owing to the presence
	of radiolysis in the crystal after an excessive radiation dose. Radiation-induced
	structural changes may interfere with the interpretation of ligand-binding
	studies or MAD data. The experiments reported here suggest that there
	is an intrinsic limit to the amount of data which can be extracted
	from a sample of a given size.},
  keywords = {Amino Acids, Animals, Carboxylic Acids, Crystallography, X-Ray, Cystine,
	Fourier Analysis, Free Radical Scavengers, Freezing, Gamma Rays,
	Glycoside Hydrolases, Hydroxyl Radical, Models, Molecular, Molecular
	Sequence Data, Synchrotrons, X-Rays, 10713520},
  owner = {brooks},
  pdf = {Burmeister-Structural_changes_in_a_cryo-cooled_protein_crystal_owing_to_radiation_damage.pdf},
  pii = {AD0099},
}

@MANUAL{ortep:96,
  title = {ORTEP-III: Oak Ridge Thermal Ellipsoid Plot Program for
 Crystal
	Structure Illustrations},
  author = {Burnett, M. N. and Johnson, C. K.},
  organization = {Oak Ridge National Laboratory Report ORNL-6895},
  year = {1996},
}

@ARTICLE{campbell-95,
  author = {J.~W. Campbell},
  title = {{XDL\_VIEW}, an X-windows-based toolkit for crystallographic and
	other applications},
  journal = jac,
  year = {1995},
  volume = {28},
  pages = {236-242},
}

@ARTICLE{castellano-etal-92,
  author = {E.~E. Castellano and G. Oliva and J. Navaza},
  title = {Fast Rigid-Body Refinement for Molecular-Replacement Techniques},
  optjournal = {#jac#},
  optnote = {amore},
  optpages = {281--284},
  optvolume = {25},
  optyear = {1992},
}

@TECHREPORT{caticha-ellis:81,
  author = {Caticha-Ellis, S.},
  title = {Anomalous Dispersion of {X}-rays in Crystallography},
  institution = {Instituto de Fisica `Gleb Wataghin' Universidade
 Estadual de Campinas
	C.P. 1170},
  year = {1981},
  number = {8},
}

@MISC{ccp4-79,
  author = {CCP4},
  title = {The {SERC} {(UK)} {C}ollaborative {C}omputing {P}roject
	
	  No.\ 4, a Suite of Programs for Protein Crystallography},
  howpublished = {Distributed from Daresbury Laboratory, Warrington
	
	  WA4~4AD, UK.},
  year = {1979},
}

@ARTICLE{Cohen2001,
  author = {SL Cohen and BT Chait},
  title = {Mass spectrometry as a tool for protein crystallography.},
  journal = {Annu Rev Biophys Biomol Struct},
  year = {2001},
  volume = {30},
  pages = {67-85},
  abstract = {Atomic resolution structure determinations of proteins by X-ray crystallography
	are formidable multidisciplinary undertakings, requiring protein
	construct design, expression and purification, crystallization trials,
	phase determination, and model building. Modern mass spectrometric
	methods can greatly facilitate these obligate tasks. Thus, mass spectrometry
	can be used to verify that the desired protein construct has been
	correctly expressed, to define compact domains in the target protein,
	to assess the components contained within the protein crystals, and
	to screen for successful incorporation of seleno-methionine and other
	heavy metal reagents used for phasing. In addition, mass spectrometry
	can be used to address issues of modeling, topology, and side-chain
	proximity. Here, we demonstrate how rational use of mass spectrometry
	assists and expedites high resolution X-ray structure determination
	through each stage of the process of protein crystallography.},
  doi = {10.1146/annurev.biophys.30.1.67},
  keywords = {Animals, Crystallography, Humans, Models, Molecular, Protein Structure,
	Tertiary, Proteins, Research Support, U.S. Gov't, P.H.S., Spectrometry,
	Mass, Matrix-Assisted Laser Desorption-Ionization, Spectrum Analysis,
	Mass, 11340052},
  owner = {brooks},
  pdf = {Cohen_Chait-Mass_Spectrometry_as_a_tool_for_crystallography.pdf},
  pii = {30/1/67},
  url = {http://dx.doi.org/10.1146/annurev.biophys.30.1.67},
}

@ARTICLE{Collaborative1994,
  author = {Collaborative Computational Project, Number 4},
  title = {The {CCP}4 suite: programs for protein crystallography.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {1994},
  volume = {50},
  pages = {760-3},
  number = {Pt 5},
  month = {Sep},
  abstract = {The CCP4 (Collaborative Computational Project, number 4) program suite
	is a collection of programs and associated data and subroutine libraries
	which can be used for macromolecular structure determination by X-ray
	crystallography. The suite is designed to be flexible, allowing users
	a number of methods of achieving their aims and so there may be more
	than one program to cover each function. The programs are written
	mainly in standard Fortran77. They are from a wide variety of sources
	but are connected by standard data file formats. The package has
	been ported to all the major platforms under both Unix and VMS. The
	suite is distributed by anonymous ftp from Daresbury Laboratory and
	is widely used throughout the world.},
  keywords = {, , 15299374},
}

@ARTICLE{coulter-71,
  author = {C. L. Coulter},
  title = {Tangent Formula Applications in Protein
	
	  Crystallography: An Evaluation},
  journal = ac,
  year = {1971},
  volume = {B27},
  pages = {1730--1740},
}

@ARTICLE{cowtan/main-93,
  author = {K. D. Cowtan and P. Main},
  title = {Improvement of Macromolecular Electron-Density Maps
	
	  by the Simultaneous Application of Real and Reciprocal Space Constraints},
  journal = ac,
  year = {1993},
  volume = {D49},
  pages = {148--157},
  optnote = {squash (/dm)},
}

@ARTICLE{Cowtan1994,
  author = {Kevin Cowtan},
  title = {'dm': An automated procedure for phase improvement by density modification.},
  journal = {Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography},
  year = {1994},
  volume = {31},
  pages = {p34-38},
}

@ARTICLE{crick/magdoff-56,
  author = { F. H. C. Crick and  B. S. Magdoff},
  title = {The Theory of the Method of Isomorphous Replacement
	
	  for Protein Crystals. {I}},
  journal = ac,
  year = {1956},
  volume = {9},
  pages = {901},
}

@ARTICLE{cromer-65,
  author = {D. T. Cromer},
  journal = ac,
  year = {1965},
  volume = {A25},
  optnote = {anomalous form factors used by mlphare},
}

@INPROCEEDINGS{crowther-72,
  author = {Crowther, R. A.},
  title = {The Fast Rotation Function},
  booktitle = {The Molecular Replacement Method},
  year = {1972},
  editor = {M. G. Rossmann},
  number = {13},
  series = {Int. Sci. Rev. Ser.},
  pages = {173--178},
  address = {New York},
  publisher = {Gordon and Breach},
}

@ARTICLE{crowther/blow-67,
  author = {Crowther, R. A. and Blow, D. M.},
  title = {A Method of Positioning a Known Molecule in an
	
	  Unknown Crystal Structure},
  journal = ac,
  year = {1967},
  volume = {23},
  pages = {544--548},
}

@ARTICLE{cullis-etal-61,
  author = {A. F. Cullis and H. Muirhead H. and M. F. Perutz  and M. G.
	
	  Rossmann and  A. C. T. North},
  journal = {Proc. Roy. Soc. A},
  year = {1961},
  volume = {265},
  pages = {15},
}

@ARTICLE{diamond-92,
  author = {R. Diamond},
  journal = {Protein Science},
  year = {1992},
  volume = {1},
  pages = {1279--1287},
  optnote = {polypose},
}

@ARTICLE{dickerson-etal-61,
  author = {R. E. Dickerson and J. C. Kendrew and B. E. Strandberg},
  title = {The Crystal Structure of Myoglobin: Phase
	
	  Determination to a Resolution of {2\,\AA} by the Method of
	
	  Isomorphous Replacement},
  journal = ac,
  year = {1961},
  volume = {14},
  pages = {1188},
}

@ARTICLE{dickerson-etal-68,
  author = {R. E. Dickerson and J. E. Weinzierl and R. A. Palmer},
  title = {A Least-Squares Refinement Method for Isomorphous
	
	  Replacement},
  journal = ac,
  year = {1968},
  volume = {24},
  pages = {997--1003},
}

@INPROCEEDINGS{dodson-75a,
  author = {E. J. Dodson},
  title = {Handling Protein Native and Derivative Data},
  booktitle = {Crystallographic Computing Techniques},
  year = {1976},
  editor = {F. R. Ahmed},
  pages = {205--211},
  address = {Copenhagen},
  publisher = {Munksgaard},
}

@INPROCEEDINGS{dodson-75b,
  author = {E. J. Dodson},
  title = {A Comparison of Different Heavy Atom Refinement Procedures},
  booktitle = {Crystallographic Computing Techniques},
  year = {1976},
  editor = {F. R. Ahmed},
  pages = {259--268},
  address = {Copenhagen},
  publisher = {Munksgaard},
}

@INPROCEEDINGS{dodson-etal-75,
  author = {E. J. Dodson and P. R. Evans and S. French},
  booktitle = {Anomalous Scattering},
  year = {1975},
  editor = {S. Ramaseshan and S. C. Abramson},
  pages = {423-436},
  address = {Copenhagen},
  publisher = {Munksgaard},
}

@BOOK{drenth,
  title = {Principles of Protein X-ray Crystallography},
  publisher = {Springer--Verlag},
  year = {1994},
  author = {Jan Drenth},
}

@ARTICLE{driessen/etal-89,
  author = {Driessen, H. and Haneef, M. I. J. and Harris,
	
	  G. W. and Howlin, B. and Khan, G. and Moss, D. S.},
  journal = jac,
  year = {1989},
  volume = {22},
  pages = {510--516},
}

@ARTICLE{Eisenberg1997,
  author = {D. Eisenberg and R. L?thy and J. U. Bowie},
  title = {V{ERIFY}3{D}: assessment of protein models with three-dimensional
	profiles.},
  journal = {Methods Enzymol},
  year = {1997},
  volume = {277},
  pages = {396-404},
  keywords = {Amino Acid Sequence, Computer Communication Networks, Computer Simulation,
	Crystallography, Hemerythrin, Immunoglobulin Variable Region, Models,
	Non-P.H.S., P.H.S., Pr, Protein Conformation, Protein Folding, Reproducibility
	of Results, Research Support, Ribulose-Bisphosphate Carboxylase,
	Structural, U.S. Gov't, X-Ray, oteins, 9379925},
  owner = {brooks},
}

@ARTICLE{engh/huber-91,
  author = {R. A. Engh and R. Huber},
  title = {Accurate bond and angle parameters for {X}-ray
	
	  protein structure refinement},
  journal = ac,
  year = {1991},
  volume = {A47},
  pages = {392--400},
  optnote = {protin dictionary},
}

@ARTICLE{fan-etal-90,
  author = {Hai--Fu Fan and Quan Hao and M. M. Woolfson},
  title = {On the Application of One-Wavelength Anomalous Scattering.
	
	   {II} An Analytical Approach for Phase Determination},
  journal = ac,
  year = {1990},
  volume = {A46},
  pages = {659--664},
}

@ARTICLE{fitzgerald-88,
  author = {P. M. D. Fitzgerald},
  title = {{MERLOT}, n Integrated Package of Computer Programs
	
	  for the Determination of Crystal Structures by Molecular
	
	  Replacement},
  journal = jac,
  year = {1988},
  volume = {21},
  pages = {273-281},
  optnote = {MERLOT},
}

@ARTICLE{fox/holmes-66,
  author = {Fox and Holmes},
  title = {An Alternative Method of Solving the Layer Scaling Equations
	
	    of Hamilton, Rollett and Sparks.},
  journal = ac,
  year = {1966},
  volume = {20},
  pages = {886--891},
  optnote = {rotavata},
}

@ARTICLE{french/wilson-78,
  author = {G. S. French and K. S. Wilson},
  journal = ac,
  year = {1978},
  volume = {A34},
  pages = {517},
  optnote = {truncate},
}

@ARTICLE{germain-etal-70,
  author = {G. Germain and P. Main and M. M. Woolfson},
  journal = ac,
  year = {1970},
  volume = {B26},
  pages = {274--285},
}

@BOOK{giacovazzo-etal,
  title = {Fundamentals of Crystallography},
  publisher = {Oxford},
  year = {1992},
  author = {Giacovazzo, C. and Monaco, H.L. and Viterbo, B.},
  series = {International Union of Crystallography Texts on Crystallocraphy},
  opteditor = {C. Giacovazzo},
}

@BOOK{glusker/trueblood,
  title = {Crystal structure analysis: a primer},
  publisher = {Oxford University Press},
  year = {1985},
  author = {Glusker, J. P. and Trueblood, K.N.},
  edition = {Second},
}

@ARTICLE{green-etal-54,
  author = {D. W. Green and V. M. Ingram and M. F. Perutz},
  journal = {Proc. Roy. Soc. A},
  year = {1954},
  volume = {225},
  pages = {287},
}

@ARTICLE{Guex1997,
  author = {N. Guex and M. C. Peitsch},
  title = {S{WISS}-{MODEL} and the {S}wiss-{P}db{V}iewer: an environment for
	comparative protein modeling.},
  journal = {Electrophoresis},
  year = {1997},
  volume = {18},
  pages = {2714-23},
  number = {15},
  month = {Dec},
  abstract = {Comparative protein modeling is increasingly gaining interest since
	it is of great assistance during the rational design of mutagenesis
	experiments. The availability of this method, and the resulting models,
	has however been restricted by the availability of expensive computer
	hardware and software. To overcome these limitations, we have developed
	an environment for comparative protein modeling that consists of
	SWISS-MODEL, a server for automated comparative protein modeling
	and of the SWISS-PdbViewer, a sequence to structure workbench. The
	Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also
	provides a large selection of structure analysis and display tools.
	In addition, we provide the SWISS-MODEL Repository, a database containing
	more than 3500 automatically generated protein models. By making
	such tools freely available to the scientific community, we hope
	to increase the use of protein structures and models in the process
	of experiment design.},
  keywords = {Amino Acid, Amino Acid Sequence, Automation, Computational Biology,
	Computer Graphics, Computer Simulation, Databases, Factual, Genome,
	Genomics, Internet, Models, Molecular, Molecular Sequence Data, Protein,
	Protein Conformation, Proteins, Reproducibility of Results, Sequence
	Alignment, Sequence Analysis, Sequence Homology, Software, Structural
	Homology, User-Computer Interface, 9504803},
}

@ARTICLE{hamilton-etal-65,
  author = {Hamilton and Rollett and Sparks},
  journal = ac,
  year = {1965},
  volume = {18},
  pages = {129--130},
  optnote = {Scala},
}

@ARTICLE{hao/woolfson-89,
  author = {Quan Hao and M. M. Woolfson},
  title = {Application of the {Ps-function} Method to Macromolecular 
	
	   Structure Determination},
  journal = ac,
  year = {1989},
  volume = {A45},
  pages = {794--797},
}

@ARTICLE{harada-etal-81,
  author = {Harada, Y. and Lifchitz, A. and Berthou, J. and Jolles, P.},
  title = {A Translation Function Combining Packing and
	
	  Diffraction Information: An Application to Lysozyme
	
	  (High-Temperature Form)},
  journal = ac,
  year = {1981},
  volume = {A37},
  pages = {398--406},
}

@ARTICLE{hart-61,
  author = {D. Harker},
  journal = ac,
  year = {1961},
  volume = {14},
  pages = {1194},
}

@ARTICLE{harker-56,
  author = {D. Harker},
  journal = ac,
  year = {1956},
  volume = {9},
  pages = {1},
}

@ARTICLE{hauptman-82,
  author = {H. Hauptman},
  title = {On Integrating the Techniques of Direct Methods and
	
	  Isomorphous Replacement.  {I.} The Theoretical Basis},
  journal = ac,
  year = {1982},
  volume = {A38},
  pages = {289-294},
  optnote = {sigmaa doc},
}

@ARTICLE{hayward/berendsen-98,
  author = {S. Hayward and H. J. C. Berendsen},
  title = {Systematic Analysis of Domain Motions in Proteins from Conformational
	Change; New Results on Citrate Synthase and T4 Lysozyme},
  journal = psfg,
  year = {1998},
  volume = {30},
  pages = {144},
}

@BOOK{helliwell,
  title = {Macromolecular Crystallography with Synchrotron radiation},
  publisher = {Cambridge University Press},
  year = {1992},
  author = {Helliwell, John R.},
  optnote = {ISBN 0521334675},
}

@ARTICLE{hendrickson-79,
  author = {W. Hendrickson},
  title = {Transformations to Optimize to Superposition of
	
	  Similar Structures},
  journal = ac,
  year = {1979},
  volume = {A35},
  pages = {158--163},
  optnote = {superpose},
}

@ARTICLE{hendrickson-91,
  author = {W. A. Hendrickson},
  title = {Determination of Macromolecular Structures from Anomalous 
	
	   Diffraction of Synchrotron Radiation},
  journal = {Science},
  year = {1991},
  volume = {254},
  pages = {51--58},
}

@ARTICLE{hendrickson/lattman-70,
  author = {W. A. Hendrickson and E. E. Lattman},
  title = {Representation of Phase Probability Distributions for
	
	  Simplified Combination of Independent Phase Informaton},
  journal = ac,
  year = {1970},
  volume = {B26},
  pages = {136--143},
}

@ARTICLE{hendrickson/teeter-81,
  author = {W. A. Hendrickson and M. M. Teeter},
  title = {Structure of the Hydrophobic Protein Crambin
	
	  Determined Directly from the Anomalous Scattering of Sulphur},
  journal = {Nature (London)},
  year = {1981},
  volume = {290},
  pages = {107--113},
}

@ARTICLE{Hodel1992,
  author = {Hodel, A. and Kim, S.-H. and Br{\"u}nger, A. T.},
  title = {{Model bias in macromolecular crystal structures}},
  journal = {Acta Crystallographica Section A},
  year = {1992},
  volume = {48},
  pages = {851--858},
  number = {6},
  month = {Nov},
  pdf = {Hodel_Brunger-Model_bias_in_macromolecular_crystal_structures.pdf},
}

@ARTICLE{Hooft1996,
  author = {R. W. Hooft and G. Vriend and C. Sander and E. E. Abola},
  title = {Errors in protein structures.},
  journal = {Nature},
  year = {1996},
  volume = {381},
  pages = {272},
  number = {6580},
  month = {May},
  keywords = {Crystallography, Databases, Factual, Protein Conformation, Quality
	Control, X-Ray, 9192890},
  owner = {brooks},
  pdf = {Hooft1996.pdf},
}

@BOOK{int-tables,
  title = {International Tables for {X}-ray Crystallography},
  publisher = {Kynoch Press},
  year = {1969},
  author = {IUCr},
  address = {Brimingham},
}

@ARTICLE{jack-etal-76,
  author = {Jack, A. and Ladner, J. E. and Klug, A.},
  title = {Crystallographic Refinement of Yeast Phenylalanine
	
	  Transfer {RNA} at {2.5\,\AA} Resolution },
  journal = {J. Mol. Biol.},
  year = {1976},
  volume = {108},
  pages = {619-649},
  optnote = {referenced by mlphare},
}

@BOOK{james-48,
  title = {The Crystalline State vol. {II}: The Optical
	
	  Principles of The Diffraction of {X}-rays},
  publisher = {G. Bell and Sons},
  year = {1948},
  author = {R. W. James},
  address = {London},
}

@TECHREPORT{jones-89,
  author = {Geraint Jones},
  title = {Deriving the fast Fourier algorithm by calculation},
  institution = {Oxford University Programming Research Group},
  year = {1989},
  type = {Technical report},
  number = {TR-4-89},
  optnote = {{\tt ftp://ftp.comlab.ox.ac.uk\slash pub\slash
	
	  Documents\slash techreports\slash TR-4-89.ps.Z}},
}

@ARTICLE{jones-78,
  author = {T. A. Jones},
  title = {A Graphics Model Building and Refinement System for
	
	  Macromolecules},
  journal = jac,
  year = {1978},
  volume = {11},
  pages = {268--272},
  optnote = {frodo},
}

@ARTICLE{jones-etal-91,
  author = {T. A. Jones and J-Y. Zou and S. W. Cowan and M. Kjeldgaard},
  title = {Improved Methods for Building Protein Models in
	
	  Electron Density Maps and the Location of Errors in these Models},
  journal = ac,
  year = {1991},
  volume = {A47},
  pages = {110--119},
  optnote = {O},
}

@ARTICLE{jones:91,
  author = {Jones, T. A. and Zou, J. Y. and Cowan, S. W. and
 Kjeldgaard, M.},
  title = {Improved methods for building protein models in electron
 density
	maps and the location of errors in these
 models},
  journal = {Acta Cryst.},
  year = {1991},
  volume = {A47},
  pages = {110-9},
}

@ARTICLE{winkler/etal-79,
  author = {Winkler F. K. and Schutt C. E. and Harrison S. C.},
  journal = ac,
  year = {1979},
  volume = {A35},
  pages = {901--911},
  optnote = {postref},
}

@ARTICLE{kabsch-88,
  author = {W. Kabsch},
  title = {Evaluation of Single-Crystal {X-ray} Diffraction
	
	  Data from a Position-Sensitive Detector},
  journal = jac,
  year = {1988},
  volume = {21},
  pages = {916--924},
  optnote = {scala},
}

@ARTICLE{kabsch-88b,
  author = {W. Kabsch},
  title = {Automatic Indexing of Rotation Diffraction Patterns},
  journal = jac,
  year = {1988},
  volume = {21},
  pages = {67--71},
  optnote = {refix},
}

@ARTICLE{kabsch-76,
  author = {W. Kabsch},
  title = {A Solution for the Best Rotation to Relate Two Sets
	
	  of Vectors},
  journal = ac,
  year = {1976},
  volume = {A32},
  pages = {922-923},
  optnote = {lsqkab},
}

@ARTICLE{kabsch/sander-83,
  author = {W. Kabsch and C. Sander},
  title = {Dictionary of protein secondary structure:
	
	pattern recognition of hydrogen-bonded and geometrical features},
  journal = {Biopolymers},
  year = {1983},
  volume = {22},
  pages = {2577--2637},
  optnote = {hbond,dssp},
}

@ARTICLE{kabsch-93,
  author = {Wolfgang Kabsch},
  title = {Automatic Processing of Rotation Diffraction Data
	
	  from Crystals of Initially Unknown Symmetry and Cell Constants},
  journal = jac,
  year = {1993},
  volume = {26},
  pages = {795--800},
  optnote = {refix},
}

@ARTICLE{karle/hauptman-56,
  author = { J. Karle and H. Hauptman},
  title = {A Theory of Phase Determination for the Four Types
	
	  of Non-Centrosymmetric Space Groups $1P222$, $2P22$, $3P_12$,
	
	  $3P_22$},
  journal = ac,
  year = {1956},
  volume = {9},
  pages = {635-651},
}

@ARTICLE{kartha/partharasarathy-65,
  author = { G. Kartha  and R. Partharasarathy},
  title = {Combination of Multiple Isomorphous Replacement and
	
	  Anomalous Dispersion Data for Protein Structure Determination. 
	{I.}
	
	  {Determination} of heavy-Atom Positions in Protein Derivatives},
  journal = ac,
  year = {1965},
  volume = {18},
  pages = {745},
}

@ARTICLE{kendrew-etal-58,
  author = {J. C. Kendrew and G. Bodo and H. M. Dintzis and R.
	
	  G. Parrish and H. Wyckoff and  D. C. Phillips},
  title = {A Three-dimensional Model of the Myoglobin Molecule
	
	  Obtained by {X-ray} Analysis},
  journal = {Nature (London)},
  year = {1958},
  volume = {181},
  pages = {662--666},
}

@ARTICLE{Kleywegt1998,
  author = {G. J. Kleywegt and T. A. Jones},
  title = {Databases in protein crystallography.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {1998},
  volume = {54},
  pages = {1119-31},
  number = {Pt 6 Pt 1},
  month = {Nov},
  abstract = {Applications of structural databases in the protein crystallographic
	structure determination process are reviewed, using mostly examples
	from work carried out by the authors. Four application areas are
	discussed: model building, model refinement, model validation and
	model analysis.},
  keywords = {, Computational Biology, Crystallography, Database Management Systems,
	Databases, Electrons, Factual, Humans, Internet, Models, Molecular,
	Non-U.S. Gov't, Protein, Protein Conformation, Protein Structure,
	Proteins, Reproducibility of Results, Research Support, Software,
	Statistics, Temperature, Tertiary, X-Ray, 10089488},
}

@ARTICLE{kleywegt/jones-96a,
  author = {G. J. Kleywegt and T. A. Jones},
  title = { },
  journal = ac,
  year = {1996},
  volume = {D52},
  pages = {826--828},
  optnote = {xdlMAPMAN and xdlDATAMAN},
}

@ARTICLE{kleywegt/jones-96b,
  author = {G. J. Kleywegt and T. A. Jones},
  title = {Efficient Rebuilding of Protein Structures},
  journal = ac,
  year = {1996},
  volume = {D52},
  pages = {829--832},
  optnote = {OOPS},
}

@ARTICLE{Kleywegt1997,
  author = {G. J. Kleywegt and R. J. Read},
  title = {Not your average density.},
  journal = {Structure},
  year = {1997},
  volume = {5},
  pages = {1557-69},
  number = {12},
  month = {Dec},
  keywords = {Crystallization, Crystallography, Mathematical Computing, Models,
	Molecular, Non-U.S. Gov't, Protein Conformation, Proteins, Research
	Support, X-Ray, 9438862},
  pdf = {Kleywegt1997.pdf},
}

@ARTICLE{Klosterman2002,
  author = {Peter S Klosterman and Makio Tamura and Stephen R Holbrook and Steven
	E Brenner},
  title = {S{COR}: a {S}tructural {C}lassification of {RNA} database.},
  journal = {Nucleic Acids Res},
  year = {2002},
  volume = {30},
  pages = {392-4},
  number = {1},
  month = {Jan},
  abstract = {The Structural Classification of RNA (SCOR) database provides a survey
	of the three-dimensional motifs contained in 259 NMR and X-ray RNA
	structures. In one classification, the structures are grouped according
	to function. The RNA motifs, including internal and external loops,
	are also organized in a hierarchical classification. The 259 database
	entries contain 223 internal and 203 external loops; 52 entries consist
	of fully complementary duplexes. A classification of the well-characterized
	tertiary interactions found in the larger RNA structures is also
	included along with examples. The SCOR database is accessible at
	http://scor.lbl.gov.},
  keywords = {Animals, Base Pairing, Base Sequence, Biomolecular, Computational
	Biology, Consensus Sequence, Conserved Sequence, Crystallography,
	Databases, Forecasting, Humans, Information Storage and Retrieval,
	Internet, Models, Molecular, Non-U.S. Gov't, Nucle, Nuclear Magnetic
	Resonance, Nucleic Acid, Nucleic Acid Conformation, P.H.S., RNA,
	Research Support, Structure-Activity Relationship, U.S. Gov't, User-Computer
	Interface, X-Ray, ic Acid Conformation, 11752346},
}

@PHDTHESIS{knight-89,
  author = {Knight, S.},
  title = {{Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase---A
	
	  Structural Study}},
  school = {Swedish University of Agricultural Sciences, Uppsala},
  year = {1989},
  optnote = {rsps},
}

@ARTICLE{kraulis-91,
  author = {P. Kraulis},
  title = {{MOLSCRIPT}: a Program to Produce Both Detailed and
	
	  Schematic Plot of Protein Structures},
  journal = jac,
  year = {1991},
  volume = {24},
  pages = {946--950},
}

@ARTICLE{kraut-etal-62,
  author = {J. Kraut and L. C. Sieker and D. F. High and S.
	
	  T. Freer },
  title = {Chymotrypsinogen: a Three-dimensional {Fourier}
	
	  Syntheis at {5\AA} Resolution},
  journal = {Proc. Nat. Acad. Sci.},
  year = {1962},
  volume = {48},
  pages = {1417-1424},
  optnote = {fhscal, vecref},
}

@BOOK{La1997,
  title = {Macromolecular Crystallography},
  publisher = {Elsevier},
  year = {1997},
  editor = {Robert M. Sweet, Charles Carter, Jr.},
  author = {La Fortelle, E. de \& Bricogne, G.},
  volume = {276},
}

@ARTICLE{ladenstein-etal-87,
  author = {R. Ladenstein and A. Bacher and R. Huber},
  title = {Some Observations of a Correlation Between the
	
	  Symmetry of Large Heavy-atom Complexes and Their Binding Sites in
	
	  Proteins},
  journal = jmb,
  year = {1987},
  volume = {195},
  pages = {751},
}

@ARTICLE{laskowski-etal-93,
  author = {R. A. Laskowski and M. W. Mac Arthur and D. S. Moss
	
	  and J. M. Thornton},
  title = {{\sc procheck}: a program to check the
	
	  stereochemical quality of protein structures},
  journal = jac,
  year = {1993},
  pages = {283--291},
  optnote = {procheck},
}

@ARTICLE{Laskowski1997,
  author = {R. A. Laskowski and E. G. Hutchinson and A. D. Michie and A. C. Wallace
	and M. L. Jones and J. M. Thornton},
  title = {P{DB}sum: a {W}eb-based database of summaries and analyses of all
	{PDB} structures.},
  journal = {Trends Biochem Sci},
  year = {1997},
  volume = {22},
  pages = {488-90},
  number = {12},
  month = {Dec},
  keywords = {Amino Acid Sequence, Computer Communication Networks, Databases, Factual,
	Molecular Sequence Data, Proteins, 9433130},
  pii = {S0968000497011407},
}

@ARTICLE{laskowski:93,
  author = {Laskowski, R. A. and Moss, D. S. and Thornton, J. M.},
  title = {Main-chain bond lengths and bond angles in protein
 structures},
  journal = {JMB},
  year = {1993},
  volume = {231},
  pages = {1049-67},
  number = {4},
}

@ARTICLE{lattman/love-70,
  author = {Lattman, E. E. and Love, W. E.},
  title = {A Rotational Search Procedure for Detecting a Known
	
	  Molecule in a Crystal},
  journal = ac,
  year = {1970},
  volume = {B26},
  pages = {1854--1857},
}

@ARTICLE{lawton-73,
  author = {S. L. Lawton},
  journal = jac,
  year = {1973},
  volume = {6},
  pages = {309--346},
  optnote = {tracer},
}

@ARTICLE{lee-pakes-69,
  author = {Lee, J. D. and Pakes, H. W.},
  title = {Revised Analytic Constants for Atomic Scattering Factors},
  journal = ac,
  year = {1969},
  volume = {A25},
  pages = {712--713},
  optnote = {referenced by mlphare (form factors)},
}

@ARTICLE{leslie-87,
  author = {A. G. W. Leslie},
  title = {A Reciprocal-Space Method for Calculating a
	
	  Molecular Envelope Using the Algorithm of {B. C. Wang}},
  journal = ac,
  year = {1987},
  volume = {A43},
  pages = {134--136},
  optnote = {flatmap},
}

@ARTICLE{Leslie1999,
  author = {AG Leslie},
  title = {Integration of macromolecular diffraction data.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {1999},
  volume = {55 ( Pt 10)},
  pages = {1696-702},
  month = {Oct},
  abstract = {Diffraction intensities can be evaluated by two distinct procedures:
	summation integration and profile fitting. Equations are derived
	for evaluating the intensities and their standard errors for both
	cases, based on Poisson statistics. These equations highlight the
	importance of the contribution of the X-ray background to the standard
	error and give an estimate of the improvement which can be achieved
	by profile fitting. Profile fitting offers additional advantages
	in allowing estimation of saturated reflections and in dealing with
	incompletely resolved diffraction spots.},
  keywords = {Crystallography, X-Ray, Databases, Microscopy, Electron, Molecular
	Conformation, Research Support, Non-U.S. Gov't, Computer Graphics,
	Crystallography, X-Ray, Fourier Analysis, Proteins, Software, Synchrotrons,
	Transferases, Crystallography, X-Ray, Macromolecular Substances,
	Poisson Distribution, Software, 10531519},
  pii = {BA0027},
}

@BOOK{luger,
  title = {Modern {X}-ray Analysis on Single Crystals},
  publisher = {Walter de Gruyter},
  year = {1980},
  author = {Peter Luger},
  address = {Berlin, New York},
  optnote = {ISBN 3--110--068303--7},
}

@ARTICLE{Luscombe2001,
  author = {N. M. Luscombe and R. A. Laskowski and J. M. Thornton},
  title = {Amino acid-base interactions: a three-dimensional analysis of protein-{DNA}
	interactions at an atomic level.},
  journal = {Nucleic Acids Res},
  year = {2001},
  volume = {29},
  pages = {2860-74},
  number = {13},
  month = {Jul},
  abstract = {To assess whether there are universal rules that govern amino acid-base
	recognition, we investigate hydrogen bonds, van der Waals contacts
	and water-mediated bonds in 129 protein-DNA complex structures. DNA-backbone
	interactions are the most numerous, providing stability rather than
	specificity. For base interactions, there are significant base-amino
	acid type correlations, which can be rationalised by considering
	the stereochemistry of protein side chains and the base edges exposed
	in the DNA structure. Nearly two-thirds of the direct read-out of
	DNA sequences involves complex networks of hydrogen bonds, which
	enhance specificity. Two-thirds of all protein-DNA interactions comprise
	van der Waals contacts, compared to about one-sixth each of hydrogen
	and water-mediated bonds. This highlights the central importance
	of these contacts for complex formation, which have previously been
	relegated to a secondary role. Although common, water-mediated bonds
	are usually non-specific, acting as space-fillers at the protein-DNA
	interface. In conclusion, the majority of amino acid-base interactions
	observed follow general principles that apply across all protein-DNA
	complexes, although there are individual exceptions. Therefore, we
	distinguish between interactions whose specificities are 'universal'
	and 'context-dependent'. An interactive Web-based atlas of side chain-base
	contacts provides access to the collected data, including analyses
	and visualisation of the three-dimensional geometry of the interactions.},
  keywords = {Amino Acid, Base Pairing, DNA, DNA-Binding Proteins, Databases, Electrostatics,
	Hydrogen Bonding, Internet, Nucleic Acid Conformation, Protein Binding,
	Protein Conformation, Sequence Homology, Software, Substrate Specificity,
	Water, 11433033},
  owner = {brooks},
}

@ARTICLE{Luscombe1997,
  author = {N. M. Luscombe and R. A. Laskowski and J. M. Thornton},
  title = {N{UCPLOT}: a program to generate schematic diagrams of protein-nucleic
	acid interactions.},
  journal = {Nucleic Acids Res},
  year = {1997},
  volume = {25},
  pages = {4940-5},
  number = {24},
  month = {Dec},
  abstract = {Proteins that bind to DNA are found in all areas of genetic activity
	within the cell. To help understand how these proteins perform their
	various functions, it is useful to analyse which residues are involved
	in binding to the DNA and how they interact with the bases and sugar-phosphate
	backbone of nucleic acids. Here we describe a program called NUCPLOT
	which can automatically identify these interactions from the 3D atomic
	coordinates of the complex from a PDB file and generate a plot that
	shows all the interactions in a schematic manner. The program produces
	a PostScript output file representing hydrogen, van der Waals and
	covalent bonds between the protein and the DNA. The resulting diagram
	is both clear and simple and allows immediate identification of important
	interactions within the structure. It also facilitates comparison
	of binding found in different structures. NUCPLOT is a completely
	automatic program, which can be used for any protein-DNA complex
	and will also work for certain protein-RNA structures.},
  keywords = {, Amino Acid, Amino Acid Sequence, Base Pairing, Computer Graphics,
	Computer Simulation, DNA, DNA-Binding Proteins, Data Interpretation,
	Database Management Systems, Databases, Electrostatics, Hydrogen
	Bonding, Internet, Macromolecular Substances, Models, Molecular,
	Molecular Sequence Data, Non-U.S. Gov't, Nucleic Acid Conformation,
	Nucleic Acids, Protein Binding, Protein Conformation, Proteins, RNA,
	RNA-Binding Proteins, Repressor Proteins, Research Support, Sequence
	Homology, Software, Statistical, Substrate Specificity, Transcription
	Factors, Water, 9396800},
  owner = {brooks},
  pdf = {Luscombe1997.pdf},
  pii = {gka795},
}

@ARTICLE{luzzati-53,
  author = {V. Luzzati},
  journal = ac,
  year = {1953},
  volume = {6},
  pages = {142--152},
  optnote = {sigmaa doc},
}

@ARTICLE{luzzati-52,
  author = {V. Luzzati},
  journal = ac,
  year = {1952},
}

@ARTICLE{matthews-68,
  author = {Matthews, B. W.},
  title = {The Solvent Content of Protein Crystals},
  journal = jmb,
  year = {1968},
  volume = {33},
  pages = {491-497},
}

@ARTICLE{matthews-66a,
  author = {B. W. Matthews},
  title = {The Extension of the Isomorphous Replacement Method
	
	  to Include Anomalous Scattering Measurements},
  journal = ac,
  year = {1966},
  volume = {20},
  pages = {82--86},
}

@ARTICLE{matthews-66b,
  author = {B. W. Matthews},
  title = {The Determination of the Position of Anomalously
	
	  Scattering Heavy Atom Groups in Protein Crystals},
  journal = ac,
  year = {1966},
  volume = {20},
  pages = {230},
}

@ARTICLE{McCoy2005,
  author = {McCoy, Airlie J. and Grosse-Kunstleve, Ralf W. and Storoni, Laurent
	C. and Read, Randy J.},
  title = {{Likelihood-enhanced fast translation functions}},
  journal = {Acta Crystallographica Section D},
  year = {2005},
  volume = {61},
  pages = {458--464},
  number = {4},
  month = {Apr},
  abstract = {This paper is a companion to a recent paper on fast rotation functions
	[Storoni et al. (2004), Acta Cryst. D60, 432-438], which showed how
	a Taylor-series expansion of the maximum-likelihood rotation function
	leads to improved likelihood-enhanced fast rotation functions. In
	a similar manner, it is shown here how linear and quadratic Taylor-series
	expansions and least-squares approximations of the maximum-likelihood
	translation function lead to likelihood-enhanced translation functions,
	which can be calculated by FFT and which are more sensitive to the
	correct translation than the traditional correlation-coefficient
	fast translation function. These likelihood-enhanced translation
	targets for molecular-replacement searches have been implemented
	in the program Phaser using the Computational},
  pdf = {McCoy2005.pdf},
}

@ARTICLE{McCoy2004,
  author = {McCoy, Airlie J. and Storoni, Laurent C. and Read, Randy J.},
  title = {{Simple algorithm for a maximum-likelihood SAD function}},
  journal = {Acta Crystallographica Section D},
  year = {2004},
  volume = {60},
  pages = {1220--1228},
  number = {7},
  month = {Jul},
  abstract = {Recently, the multivariate complex normal distribution has been used
	to develop a maximum-likelihood probability function for single-wavelength
	anomalous diffraction phasing and refinement of heavy-atom parameters
	[Pannu & Read (2004), Acta Cryst. D60, 22-27]. The function accounts
	explicitly for the correlations between the observed and calculated
	Friedel mates and their errors. However, the method of derivation
	of the equation described by Pannu & Read (2004) leads to a complicated
	likelihood expression that suffers from a number of algorithmic limitations.
	Here, an alternative derivation of the PSAD function is described
	that leads to simplified algorithmic requirements and that allows
	an intuitive understanding of the expression.},
  pdf = {Read2003.pdf},
}

@ARTICLE{McGuffin2000,
  author = {LJ McGuffin and K Bryson and DT Jones},
  title = {The {PSIPRED} protein structure prediction server.},
  journal = {Bioinformatics},
  year = {2000},
  volume = {16},
  pages = {404-5},
  number = {4},
  month = {Apr},
  abstract = {SUMMARY: The PSIPRED protein structure prediction server allows users
	to submit a protein sequence, perform a prediction of their choice
	and receive the results of the prediction both textually via e-mail
	and graphically via the web. The user may select one of three prediction
	methods to apply to their sequence: PSIPRED, a highly accurate secondary
	structure prediction method; MEMSAT 2, a new version of a widely
	used transmembrane topology prediction method; or GenTHREADER, a
	sequence profile based fold recognition method. AVAILABILITY: Freely
	available to non-commercial users at http://globin.bio.warwick.ac.uk/psipred/},
  keywords = {Protein Folding, Protein Structure, Secondary, Proteins, Software,
	10869041},
  owner = {brooks},
  pdf = {McGuffin_Jones-The_PSIPRED_protein_structure_prediction_server.pdf},
}

@BOOK{mcree-93,
  title = {Practical protein crystallography},
  publisher = {Academic Press},
  year = {1993},
  author = {Mc~Ree, Duncan E.},
  optnote = {XtalView},
}

@ARTICLE{merritt:99,
  author = {Merritt, E. A.},
  title = {Expanding the model: anisotropic displacement parameters in
 protein
	structure refinement},
  journal = {Acta Cryst.},
  year = {1999},
  volume = {D55},
  pages = {1109-1117},
}

@ARTICLE{mukherjee-etal-89,
  author = {A. K. Mukherjee and J. R. Helliwell and P. Main},
  title = {The use of {MULTAN} to Locate the Positions of Anomalous 
	
	   Scatterers},
  journal = ac,
  year = {1989},
  volume = {A45},
  pages = {715--718},
}

@ARTICLE{murshudov-etal-97,
  author = {G. N. Murshudov and A. A. Vagin and E. J. Dodson},
  title = {Refinement of Macromolecular Structures by the Maximum-Likelihood
	Method},
  journal = ac,
  year = {1997},
  volume = {D53},
  pages = {240-253},
}

@ARTICLE{Murshudov1997,
  author = {G. N. Murshudov and A. A. Vagin and E. J. Dodson},
  title = {Refinement of macromolecular structures by the maximum-likelihood
	method.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {1997},
  volume = {53},
  pages = {240-55},
  number = {Pt 3},
  month = {May},
  abstract = {This paper reviews the mathematical basis of maximum likelihood. The
	likelihood function for macromolecular structures is extended to
	include prior phase information and experimental standard uncertainties.
	The assumption that different parts of a structure might have different
	errors is considered. A method for estimating sigma(A) using 'free'
	reflections is described and its effects analysed. The derived equations
	have been implemented in the program REFMAC. This has been tested
	on several proteins at different stages of refinement (bacterial
	alpha-amylase, cytochrome c', cross-linked insulin and oligopeptide
	binding protein). The results derived using the maximum-likelihood
	residual are consistently better than those obtained from least-squares
	refinement.},
  doi = {10.1107/S0907444996012255},
  keywords = {, , 15299926},
  pii = {S0907444996012255},
  url = {http://dx.doi.org/10.1107/S0907444996012255},
}

@ARTICLE{navaza-94,
  author = {J. Navaza},
  title = {{AMoRe}: an Automated Package for Molecular Replacement},
  journal = ac,
  year = {1994},
  volume = {A50},
  pages = {157--163},
  optnote = {AMoRe (main reference)},
}

@ARTICLE{navaza-93,
  author = {J. Navaza},
  title = {On the Computation of the Fast Rotation Function},
  journal = ac,
  year = {1993},
  volume = {D49},
  pages = {588--591},
}

@ARTICLE{navaza-90,
  author = {J. Navaza},
  title = {Accurate Computation of the Rotation Matrices},
  journal = ac,
  year = {1990},
  volume = {A46},
  pages = {619--620},
  optnote = {AMoRe},
}

@ARTICLE{navaza-87,
  author = {J. Navaza},
  title = {On the Fast Rotation Function},
  journal = ac,
  year = {1987},
  volume = {A43},
  pages = {645--653},
  optnote = {AmoRe},
}

@ARTICLE{navaza/vernoslova-95,
  author = {J. Navaza and E. Vernoslova},
  title = {On the Fast Translation Function for Molecular Replacement},
  journal = ac,
  year = {1995},
  volume = {A51},
  pages = {445-449},
  optnote = {New `CO' TF which IJT says is equivalent to tffc with Es},
}

@ARTICLE{nixon/north-76,
  author = {Nixon, P. E. and North, A. C. T.},
  title = {Crystallographic Relationship Between Human and
	
	  Hen-Egg Lysozymes. {I.} Methods for the Establishment of Molecular
	
	  Orientational and Positional Parameters},
  journal = ac,
  year = {1976},
  volume = {A32},
  pages = {320--325},
}

@ARTICLE{iupac-70,
  author = {IUPAC-IUB Commission on Biochemical Nomenclature},
  title = {Abbreviations and
	
	symbols for the description of the conformation of polypeptide chains},
  journal = jmb,
  year = {1970},
  volume = {52},
  pages = {1--17},
  optnote = {rwbrook},
}

@ARTICLE{north-65,
  author = {A. C. T. North},
  title = {The Combination of Isomorphous Replacement and
	
	  Anomalous Scattering Data in Phase Determination of
	
	  Non-Centrosymmetric Reflexions},
  journal = ac,
  year = {1965},
  volume = {18},
  pages = {212--216},
}

@ARTICLE{o'halloran-etal-87,
  author = {O' Halloran, T. V. and S. J. Lippard and T. J.
	
	  Richmond and A. Klug},
  title = {Multiple HEavy-atom Reagents for Macromolecular {X-ray} Structure
	Dtermination},
  journal = jmb,
  year = {1987},
  volume = {194},
  optpages = {705-712},
}

@INCOLLECTION{otwinowski:97,
  author = {Otwinowski, Z. and Minor, W.},
  title = {Processing of {X}-ray Diffraction Data Collected in
 Oscillation
	Mode},
  booktitle = {Methods Enzymol.},
  publisher = {Academic Press},
  year = {1997},
  editor = {Carter, Jr, C. W. and Sweet, R. M.},
  volume = {276},
  pages = {307-326},
  address = {New York},
  edition = {{M}acromolecular {C}rystallography, {P}art {A}},
}

@ARTICLE{drieesen/tickle-94,
  author = {Huub P.~C.~Driessen and Ian J.~Tickle},
  title = {The use of normalised amplitudes in the Rotation Function},
  journal = {Joint {CCP4} and {ESF--EACBM} Newsletter on Protein
	
	  Crystallography},
  year = {1994},
  number = {30},
  month = {June},
}

@ARTICLE{Pannu2004,
  author = {Navraj S Pannu and Randy J Read},
  title = {The application of multivariate statistical techniques improves single-wavelength
	anomalous diffraction phasing.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {2004},
  volume = {60},
  pages = {22-7},
  number = {Pt 1},
  month = {Jan},
  abstract = {Recently, there has been a resurgence in phasing using the single-wavelength
	anomalous diffraction (SAD) experiment; data from a single wavelength
	in combination with techniques such as density modification have
	been used to solve macromolecular structures, even with a very small
	anomalous signal. Here, a formulation for SAD phasing and refinement
	employing multivariate statistical techniques is presented. The equation
	developed accounts explicitly for the correlations among the observed
	and calculated Friedel mates in a SAD experiment. The correlated
	SAD equation has been implemented and test cases performed on real
	diffraction data have revealed better results compared with currently
	used programs in terms of correlation with the final map and obtaining
	more reliable phase probability statistics.},
  keywords = {Crystallography, X-Ray, DNA, Data Interpretation, Statistical, Multivariate
	Analysis, Muramidase, Research Support, Non-U.S. Gov't, 14684888},
  owner = {brooks},
  pdf = {PannuRead_TheApplicationOfMultivariateStatisticalTechniquesImprovesSingleWavelengthAnomalousDiffractionPhasing.pdf},
  pii = {S0907444903020808},
}

@ARTICLE{Pannu2003,
  author = {Pannu, Navraj S. and McCoy, Airlie J. and Read, Randy J.},
  title = {{Application of the complex multivariate normal distribution to crystallographic
	methods with insights into multiple isomorphous replacement phasing}},
  journal = {Acta Crystallographica Section D},
  year = {2003},
  volume = {59},
  pages = {1801--1808},
  number = {10},
  month = {Oct},
  pdf = {Pannu2003.pdf},
}

@ARTICLE{Pannu1998,
  author = {NS Pannu and GN Murshudov and EJ Dodson and RJ Read},
  title = {Incorporation of prior phase information strengthens maximum-likelihood
	structure refinement.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {1998},
  volume = {54},
  pages = {1285-94},
  number = {Pt 6 Pt 2},
  month = {Nov},
  abstract = {The application of a maximum-likelihood analysis to the problem of
	structure refinement has led to striking improvements over the traditional
	least-squares methods. Since the method of maximum likelihood allows
	for a rational incorporation of other sources of information, we
	have derived a likelihood function that incorporates experimentally
	determined phase information. In a number of different test cases,
	this target function performs better than either a least-squares
	target or a maximum-likelihood function lacking prior phases. Furthermore,
	this target gives significantly better results compared with other
	functions incorporating phase information. When combined with a procedure
	to mask 'unexplained' density, the phased likelihood target also
	makes it possible to refine very incomplete models.},
  keywords = {Animals, Crystallography, X-Ray, Cytochrome c Group, Likelihood Functions,
	Models, Molecular, Molecular Structure, Protein Conformation, Receptors,
	Estrogen, Research Support, Non-U.S. Gov't, 10089505},
  owner = {brooks},
  pdf = {PannuRead_IncorporationOfPriorPhaseInformationStrengthensMaximum-LikelihoodStructureRefinement.pdf},
}

@ARTICLE{perutz-56,
  author = {M. F. Perutz},
  title = {Isomorphous Replacement and Phase Determination in
	
	  Non-centrosymmetric Space Groups},
  journal = ac,
  year = {1956},
  volume = {9},
  pages = {867},
}

@BOOK{perutz,
  title = {Protein structure: new approaches to disease and therapy},
  publisher = {W.H. Freeman and Co},
  year = {1992},
  author = {Max Perutz},
  address = {New York},
  optnote = {ISBN 0--7167--7022--9},
}

@ARTICLE{podjarny-etal-87,
  author = {Podjarny, A.D. and Bhat, T.N. and Zwick, M.},
  title = {Improving Crystallographic Macromolecular Images:
	
	  the Real-space Approach},
  journal = {Ann. Rev. Biophys. Biophys. Chem.},
  year = {1987},
  volume = {16},
  pages = {351--373},
}

@BOOK{numerical-recipes,
  title = {Numerical Recipes: The Art of Scientific Computing},
  publisher = {Cambridge Scientific Press},
  year = {1986},
  author = {Press, W. H. and Flannery, B. P. and Teukolsky, S.
	
	  A. and Vetterling, W. T.},
}

@ARTICLE{priestle-93,
  author = {J. P. Priestle},
  title = {Standard Stereochemical Dictionaries for Protein
	
	  Structure Refinement and Model Building},
  journal = {Joint {CCP4} and {ESF--EACBM} Newsletter on Protein
	
	  Crystallography},
  year = {1993},
  number = {29},
  month = {November},
}

@ARTICLE{priestle-88,
  author = {John P. Priestle},
  title = {{RIBBON:} a stereo cartoon drawing program for proteins},
  journal = jac,
  year = {1988},
  volume = {21},
  pages = {572--576},
  optnote = {ribbon},
}

@INBOOK{busing/levy-61,
  title = {Computing Methods and the Phase Problem in {X}-ray
	
	  Crystal Analysis},
  publisher = {Pergamon},
  year = {1961},
  author = {Busing W. R. and Levy H. A.},
  optnote = {vecref},
}

@ARTICLE{ralph/woolfson-91,
  author = {A. C. Ralph and M. M. Woolfson},
  title = {On the Application of One-Wavelength Anomalous Scattering.
	
	   {III} The {Wilson and MPS} Method.},
  journal = ac,
  year = {1991},
  volume = {A47},
  pages = {533--537},
}

@ARTICLE{Ravelli2003,
  author = {Raimond B G Ravelli and Hanna-Kirsti Schr?der Leiros and Baocheng
	Pan and Martin Caffrey and Sean McSweeney},
  title = {Specific radiation damage can be used to solve macromolecular crystal
	structures.},
  journal = {Structure (Camb)},
  year = {2003},
  volume = {11},
  pages = {217-24},
  number = {2},
  month = {Feb},
  abstract = {The use of third generation synchrotron sources has led to renewed
	concern about the effect of ionizing radiation on crystalline biological
	samples. In general, the problem is seen as one to be avoided. However,
	in this paper, it is shown that, far from being a hindrance to successful
	structure determination, radiation damage provides an opportunity
	for phasing macromolecular structures. This is successfully demonstrated
	for both a protein and an oligonucleotide, by way of which complete
	models were built automatically. The possibility that, through the
	exploitation of radiation damage, the phase problem could become
	less of a barrier to macromolecular crystal structure determination
	is discussed.},
  keywords = {Crystallography, X-Ray, Macromolecular Substances, Oligonucleotides,
	Proteins, Research Support, U.S. Gov't, Non-P.H.S., Research Support,
	U.S. Gov't, P.H.S., Synchrotrons, 12575941},
  owner = {brooks},
  pdf = {RavelliMcSweeney_SpecificRadiationDamageCanBeUsedtoSolveMacromolecularCrystalStructures.pdf},
  pii = {S0969212603000066},
}

@ARTICLE{Ravelli2000,
  author = {RB Ravelli and SM McSweeney},
  title = {The 'fingerprint' that {X}-rays can leave on structures.},
  journal = {Structure Fold Des},
  year = {2000},
  volume = {8},
  pages = {315-28},
  number = {3},
  month = {Mar},
  abstract = {BACKGROUND: Exposure of biomacromolecules to ionising radiation results
	in damage that is initiated by free radicals and progresses through
	a variety of mechanisms. A widely used technique to study the three-dimensional
	structures of biomacromolecules is crystallography, which makes use
	of ionising X-rays. It is crucial to know to what extent structures
	determined using this technique might be biased by the inherent radiation
	damage. RESULTS: The consequences of radiation damage have been investigated
	for three dissimilar proteins. Similar results were obtained for
	each protein, atomic B factors increase, unit-cell volumes increase,
	protein molecules undergo slight rotations and translations, disulphide
	bonds break and decarboxylation of acidic residues occurs. All of
	these effects introduce non-isomorphism. The absorbed dose in these
	experiments can be reached during routine data collection at undulator
	beamlines of third generation synchrotron sources. CONCLUSIONS: X-rays
	can leave a 'fingerprint' on structures, even at cryogenic temperatures.
	Serious non-isomorphism can be introduced, thus hampering multiple
	isomorphous replacement (MIR) and multiwavelength anomalous dispersion
	(MAD) phasing methods. Specific structural changes can occur before
	the traditional measures of radiation damage have signalled it. Care
	must be taken when assigning structural significance to features
	that might easily be radiation-damage-induced changes. It is proposed
	that the electron-affinic disulphide bond traps electrons that migrate
	over the backbone of the protein, and that the sidechains of glutamic
	acid and aspartic acid donate electrons to nearby electron holes
	and become decarboxylated successively. The different disulphide
	bonds in each protein show a clear order of susceptibility, which
	might well relate to their intrinsic stability.},
  keywords = {Fourier Analysis, Proteins, Research Support, Non-U.S. Gov't, X-Rays,
	10745008},
  owner = {brooks},
  pdf = {Ravelli_McSweeney-The_fingerprint_that_X-rays_can_leave_on_structures.pdf},
  pii = {st8305},
}

@ARTICLE{Read1990,
  author = {Read, R. J.},
  title = {{Structure-factor probabilities for related structures}},
  journal = {Acta Crystallographica Section A},
  year = {1990},
  volume = {46},
  pages = {900--912},
  number = {11},
  month = {Nov},
  pdf = {Read1990.pdf},
}

@ARTICLE{read-86,
  author = {Read, R. J.},
  title = {Improved {Fourier} Coefficients for Maps Using
	
	  Phases from Partial Structures with Errors},
  journal = ac,
  year = {1986},
  volume = {A42},
  pages = {140--149},
  optnote = {sigmaa},
}

@ARTICLE{Read1986,
  author = {Read, R. J.},
  title = {{Improved Fourier coefficients for maps using phases from partial
	structures with errors}},
  journal = {Acta Crystallographica Section A},
  year = {1986},
  volume = {42},
  pages = {140--149},
  number = {3},
  month = {May},
  pdf = {Read1986.pdf},
}

@ARTICLE{read:86,
  author = {Read, R. J.},
  title = {Improved {F}ourier coefficients for maps using phases from
 partial
	structures with errors},
  journal = {Acta Cryst.},
  year = {1986},
  volume = {A42},
  pages = {140-149},
}

@ARTICLE{Read1988,
  author = {Read, R. J. and Schierbeek, A. J.},
  title = {{A phased translation function}},
  journal = {Journal of Applied Crystallography},
  year = {1988},
  volume = {21},
  pages = {490--495},
  number = {5},
  month = {Oct},
  pdf = {Read1988.pdf},
}

@ARTICLE{Read2003,
  author = {Read, Randy J.},
  title = {{New ways of looking at experimental phasing}},
  journal = {Acta Crystallographica Section D},
  year = {2003},
  volume = {59},
  pages = {1891--1902},
  number = {11},
  month = {Nov},
  pdf = {Read2003.pdf},
}

@ARTICLE{Read2001,
  author = {Read, Randy J.},
  title = {{Pushing the boundaries of molecular replacement with maximum likelihood}},
  journal = {Acta Crystallographica Section D},
  year = {2001},
  volume = {57},
  pages = {1373--1382},
  number = {10},
  month = {Oct},
  pdf = {Read2001.pdf},
}

@ARTICLE{Read1999,
  author = {Read, Randy J.},
  title = {{Detecting outliers in non-redundant diffraction data}},
  journal = {Acta Crystallographica Section D},
  year = {1999},
  volume = {55},
  pages = {1759--1764},
  number = {10},
  month = {Oct},
  abstract = {Outliers are observations which are very unlikely to be correct, as
	judged by independent observations or other prior information. Such
	unexpected observations are treated, effectively, as being more informative
	about possible models, so they can seriously impede the course of
	structure determination and refinement. The best way to detect and
	eliminate outliers is to collect highly redundant data, but it is
	not always possible to make multiple measurements of every reflection.
	For non-redundant data, the prior expectation given either by a Wilson
	distribution of intensities or model-based structure-factor probability
	distributions can be used to detect outliers. This captures mostly
	the excessively strong reflections, which dominate the features of
	electron-density maps or, even more so, Patterson maps. The outlier
	rejection tests have been implemented in a program, Outliar},
  pdf = {Read1999.pdf},
}

@ARTICLE{read-schierbeek-88,
  author = {Randy J. Read and Abraham J. Schierbeek},
  title = {A Phased Translation Function},
  journal = jac,
  year = {1988},
  volume = {21},
  pages = {490-495},
  optnote = {fft},
}

@BOOK{rhodes,
  title = {Crystallography Made Crystal Clear: A Guide for Users of
	
	                 Macromolecular Models},
  publisher = {Academic Press},
  year = {1993},
  author = {Gale Rhodes},
  address = {San Diego; London},
  optnote = {ISBN 0--12--587075},
}

@INCOLLECTION{rogers-85,
  author = {D. Rogers},
  booktitle = {Computing Methods in Crystallography},
  publisher = {Pergamon Press},
  year = {1985},
  editor = {J. S. Rollet},
  pages = {126--127},
  optnote = {sigmaa doc},
}

@ARTICLE{Rosenfeld1992,
  author = {J Rosenfeld and J Capdevielle and JC Guillemot and P Ferrara},
  title = {In-gel digestion of proteins for internal sequence analysis after
	one- or two-dimensional gel electrophoresis.},
  journal = {Anal Biochem},
  year = {1992},
  volume = {203},
  pages = {173-9},
  number = {1},
  month = {May},
  abstract = {We examined the different steps necessary for the enzymatic digestion
	of proteins in the polyacrylamide matrix after gel electrophoresis.
	As a result, we developed an improved method for obtaining peptides
	for internal sequence analysis from 1-2 micrograms of in-gel-digested
	proteins. The long washing-lyophilization-equilibration steps necessary
	to eliminate the dye, sodium dodecyl sulfate, and other gel-associated
	contaminants that perturb protein digestion in Coomassie blue-stained
	gels have been replaced by washing for 40 min with 50\% acetonitrile,
	drying for 10 min at room temperature, and then rehydrating with
	a protease solution. The washing and drying steps result in a substantial
	reduction of the gel slice volume that, when next swollen in the
	protease solution, readily absorbs the enzyme, facilitating digestion.
	The Coomassie blue staining procedure has also been modified by reducing
	acetic acid and methanol concentrations in the staining solution
	and by eliminating acetic acid in the destaining solution. The peptides
	resulting from the in-gel digestion are easily recovered by passive
	elution, in excellent yields for structural characterization. This
	simple and rapid method has been successfully applied for the internal
	sequence analysis of membrane proteins from the rat mitochondria
	resolved in preparative two-dimensional gel electrophoresis.},
  keywords = {Amino Acid Sequence, Chromatography, High Pressure Liquid, Electrophoresis,
	Gel, Two-Dimensional, Electrophoresis, Polyacrylamide Gel, Molecular
	Sequence Data, Peptide Fragments, Proteins, Rosaniline Dyes, Support,
	Non-U.S. Gov't, Trypsin, 1524213},
  owner = {brooks},
}

@ARTICLE{rosenfield:78,
  author = {Rosenfield, Jr, R. E. and Trueblood, N. and Dunitz,
 J. D.},
  title = {A test for rigid-body vibrations, based on a generalization
 of {H}irshfeld's
	`rigid-bond' postulate},
  journal = {Acta Cryst.},
  year = {1978},
  volume = {A34},
  pages = {828-829},
}

@ARTICLE{rossmann-61,
  author = {M. G. Rossmann},
  title = {The Position of Anomalous Scatterers in Protein Crystals},
  journal = ac,
  year = {1961},
  volume = {14},
  pages = {383--388},
}

@ARTICLE{rossmann-60,
  author = {M. G. Rossmann},
  title = {The Accurate Determination of the Position and Shape
	
	  of Heavy-Atom Replacement Groups in Proteins},
  journal = ac,
  year = {1960},
  volume = {13},
  pages = {221},
}

@ARTICLE{rossmann-etal-86,
  author = {M. G. Rossmann and E. Arnold and G. Vriend },
  title = {Comparison of Vector Search and Feedback Methods for
	
	  Finding Heavy-Atom Sites in Isomorphous Derivatives},
  journal = ac,
  year = {1986},
  volume = {A42},
  pages = {325--334},
}

@ARTICLE{rossmann/tollin-66,
  author = {Rossmann, M. G. and Tollin, P.},
  title = {A Description of Various Rotation Function Programs},
  journal = ac,
  year = {1966},
  volume = {21},
  pages = {872},
}

@ARTICLE{rossmann-90,
  author = {Michael G. Rossmann},
  title = {The Molecular Replacement Method},
  journal = ac,
  year = {1990},
  volume = {A46},
  pages = {73--82},
  optnote = {useful review?},
}

@ARTICLE{sayre-74,
  author = {D. Sayre},
  journal = ac,
  year = {1974},
  volume = {A30},
  pages = {180--184},
  optnote = {dm},
}

@ARTICLE{Schwede2003,
  author = {Torsten Schwede and J?rgen Kopp and Nicolas Guex and Manuel C Peitsch},
  title = {S{WISS}-{MODEL}: {A}n automated protein homology-modeling server.},
  journal = {Nucleic Acids Res},
  year = {2003},
  volume = {31},
  pages = {3381-5},
  number = {13},
  month = {Jul},
  abstract = {SWISS-MODEL (http://swissmodel.expasy.org) is a server for automated
	comparative modeling of three-dimensional (3D) protein structures.
	It pioneered the field of automated modeling starting in 1993 and
	is the most widely-used free web-based automated modeling facility
	today. In 2002 the server computed 120 000 user requests for 3D protein
	models. SWISS-MODEL provides several levels of user interaction through
	its World Wide Web interface: in the 'first approach mode' only an
	amino acid sequence of a protein is submitted to build a 3D model.
	Template selection, alignment and model building are done completely
	automated by the server. In the 'alignment mode', the modeling process
	is based on a user-defined target-template alignment. Complex modeling
	tasks can be handled with the 'project mode' using DeepView (Swiss-PdbViewer),
	an integrated sequence-to-structure workbench. All models are sent
	back via email with a detailed modeling report. WhatCheck analyses
	and ANOLEA evaluations are provided optionally. The reliability of
	SWISS-MODEL is continuously evaluated in the EVA-CM project. The
	SWISS-MODEL server is under constant development to improve the successful
	implementation of expert knowledge into an easy-to-use server.},
  keywords = {Computer Graphics, Internet, Models, Molecular, Protein, Proteins,
	Sequence Alignment, Sequence Analysis, Software, Structural Homology,
	User-Computer Interface, 12824332},
}

@INCOLLECTION{sheldrick:97,
  author = {Sheldrick, G. M. and Schneider, T. R.},
  title = {{SHELXL}: high-resolution refinement},
  booktitle = {Methods Enzymol.},
  publisher = {Academic Press},
  year = {1997},
  editor = {Carter, Jr, C. W. and Sweet, R. M.},
  volume = {277},
  pages = {319-343},
  address = {San Diego, CA},
  edition = {{M}acromolecular {C}rystallography, {P}art {B}},
}

@ARTICLE{sheldrick-etal-93,
  author = {Sheldrick, G. M.and Dauter, Z. and Wilson, K. S.and
	
	  Hope, H. and Sieker, L.C.},
  journal = ac,
  year = {1993},
  volume = {D49},
  pages = {18--23},
  optnote = {SHELXS-90 Pattersons and direct methods},
}

@ARTICLE{sigler/blow-65,
  author = {P. B. Sigler and D. M. Blow},
  title = {A Means of Promoting Heavy-atom Binding in Protein Crystals},
  journal = jmb,
  year = {1965},
  volume = {14},
  pages = {640--644},
}

@ARTICLE{sim-60,
  author = {G. A. Sim},
  title = {The Cumulative Distribution o Structure Amplitudes},
  journal = ac,
  year = {1960},
  volume = {13},
  optnote = {Sigmaa doc},
  optpages = {511--512},
}

@ARTICLE{sim-59,
  author = {G. A. Sim},
  title = {The Distribution of Phase Angles for Structures Containing
	
	Heavy Atoms. {II.} {A} Modification of the Normal Heavy-Atom Method
	for 
	
	Non-Centrosymmetric Structures},
  journal = ac,
  year = {1959},
  volume = {12},
  pages = {813--815},
  optnote = {Sigmaa doc},
}

@ARTICLE{singh/ramaseshan-66,
  author = {A. K. Singh and S. Ramaseshan},
  title = {The Determination of Heavy Atom Positions in Protein
	
	  Derivatives},
  journal = ac,
  year = {1966},
  volume = {21},
  pages = {279-280},
}

@ARTICLE{smith/howell-92,
  author = {David Smith and Lin Howell},
  title = {Identification of Heavy-atom Derivatives by Normal
	
	  Probability Methods},
  journal = jac,
  year = {1992},
  volume = {25},
  pages = {81--86},
}

@ARTICLE{srinivasan-66,
  author = {R. Srinivasan},
  title = {Weighting Functions for Use in the Early Stages of
	
	  Structure Analysis When a Part of the Structure is Known},
  journal = ac,
  year = {1966},
  volume = {20},
  pages = {143--144},
  optnote = {sigmaa doc},
}

@ARTICLE{steitz-68,
  author = {T. A. Steitz},
  journal = ac,
  year = {1968},
  volume = {B24},
  pages = {504},
}

@MANUAL{steitz-unpub,
  author = {T. A. Steitz},
  optnote = {Unpublished results},
}

@ARTICLE{Storoni2004,
  author = {Storoni, Laurent C. and McCoy, Airlie J. and Read, Randy J.},
  title = {{Likelihood-enhanced fast rotation functions}},
  journal = {Acta Crystallographica Section D},
  year = {2004},
  volume = {60},
  pages = {432--438},
  number = {3},
  month = {Mar},
  pdf = {Storoni2004.pdf},
}

@BOOK{stout/jensen,
  title = {{X}-ray Structure Determination: a practical guide},
  publisher = {John Wiley},
  year = {1989},
  author = {Stout, George H. and Jensen, Lyle H.},
  address = {New York},
  edition = {Second},
}

@ARTICLE{swanson-94,
  author = {S. Swanson},
  journal = ac,
  year = {1994},
  volume = {D50},
  pages = {695--708},
}

@ARTICLE{sygusch-77,
  author = {J. Sygusch},
  title = {Minimum-Variance {Fourier} Coefficients from the
	
	  Isomorphous Replacement Method by Least-Squares Analysis},
  journal = ac,
  year = {1977},
  volume = {A33},
  pages = {512--518},
}

@ARTICLE{cromer-83,
  author = {Don T.~Cromer},
  title = {Calculation of Anomalous Scattering Factors at Arbitrary Wavelengths},
  journal = jac,
  year = {1983},
  volume = {16},
  pages = {437--438},
  optnote = {crossec},
}

@ARTICLE{teneyck-77,
  author = {Ten Eyck, Lynn F.},
  title = {Efficient Structure-Factor Calculation for Large
	
	  Molecules by the Fast Fourier Transform},
  journal = ac,
  year = {1977},
  volume = {A33},
  pages = {486--492},
}

@ARTICLE{teneyck-73,
  author = {Ten Eyck, Lynn F.},
  title = {Crystallographic Fast Fourier Transforms},
  journal = ac,
  year = {1973},
  volume = {A29},
  pages = {183--191},
}

@ARTICLE{Terwilliger2001,
  author = {T. C. Terwilliger},
  title = {Map-likelihood phasing.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {2001},
  volume = {57},
  pages = {1763-75},
  number = {Pt 12},
  month = {Dec},
  abstract = {The recently developed technique of maximum-likelihood density modification
	[Terwilliger (2000), Acta Cryst. D56, 965-972] allows a calculation
	of phase probabilities based on the likelihood of the electron-density
	map to be carried out separately from the calculation of any prior
	phase probabilities. Here, it is shown that phase-probability distributions
	calculated from the map-likelihood function alone can be highly accurate
	and that they show minimal bias towards the phases used to initiate
	the calculation. Map-likelihood phase probabilities depend upon expected
	characteristics of the electron-density map, such as a defined solvent
	region and expected electron-density distributions within the solvent
	region and the region occupied by a macromolecule. In the simplest
	case, map-likelihood phase-probability distributions are largely
	based on the flatness of the solvent region. Though map-likelihood
	phases can be calculated without prior phase information, they are
	greatly enhanced by high-quality starting phases. This leads to the
	technique of prime-and-switch phasing for removing model bias. In
	prime-and-switch phasing, biased phases such as those from a model
	are used to prime or initiate map-likelihood phasing, then final
	phases are obtained from map-likelihood phasing alone. Map-likelihood
	phasing can be applied in cases with solvent content as low as 30\%.
	Potential applications of map-likelihood phasing include unbiased
	phase calculation from molecular-replacement models, iterative model
	building, unbiased electron-density maps for cases where 2F(o) -
	F(c) or sigma(A)-weighted maps would currently be used, structure
	validation and ab initio phase determination from solvent masks,
	non-crystallographic symmetry or other knowledge about expected electron
	density.},
  keywords = {Computer-Assisted, Crystallography, Electrons, Electrostatics, Image
	Processing, Likelihood Functions, Models, Molecular, Non-P.H.S.,
	P.H.S., Protein Conformation, Proteins, Reproducibility of Results,
	Research Support, U.S. Gov't, X-Ray, 11717488},
  pii = {S0907444901013749},
}

@ARTICLE{Terwilliger2000,
  author = {T. C. Terwilliger},
  title = {Maximum-likelihood density modification.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {2000},
  volume = {56 ( Pt 8)},
  pages = {965-72},
  month = {Aug},
  abstract = {A likelihood-based approach to density modification is developed that
	can be applied to a wide variety of cases where some information
	about the electron density at various points in the unit cell is
	available. The key to the approach consists of developing likelihood
	functions that represent the probability that a particular value
	of electron density is consistent with prior expectations for the
	electron density at that point in the unit cell. These likelihood
	functions are then combined with likelihood functions based on experimental
	observations and with others containing any prior knowledge about
	structure factors to form a combined likelihood function for each
	structure factor. A simple and general approach to maximizing the
	combined likelihood function is developed. It is found that this
	likelihood-based approach yields greater phase improvement in model
	and real test cases than either conventional solvent flattening and
	histogram matching or a recent reciprocal-space solvent-flattening
	procedure [Terwilliger (1999), Acta Cryst. D55, 1863-1871].},
  keywords = {Computational Biology, Crystallography, Electrostatics, Likelihood
	Functions, Macromolecular Substances, Mathematical Computing, Models,
	Molecular, Multivariate Analysis, Non-U.S. Gov't, Protein Conformation,
	Reproducibility of Results, Research Support, Solvents, Theoretical,
	X-Ray, 10944333},
  pii = {S0907444900005072},
}

@ARTICLE{Terwilliger1999a,
  author = {T. C. Terwilliger},
  title = {Reciprocal-space solvent flattening.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {1999},
  volume = {55},
  pages = {1863-71},
  number = {11},
  month = {Nov},
  abstract = {Solvent flattening is a powerful tool for improving crystallographic
	phases for macromolecular structures obtained at moderate resolution,
	but uncertainties in the optimal weighting of experimental phases
	and modified phases make it difficult to extract all the phase information
	possible. Solvent flattening is essentially an iterative method for
	maximizing a likelihood function which consists of (i) experimental
	phase information and (ii) information on the likelihood of various
	arrangements of electron density in a map, but the likelihood function
	is generally not explicitly defined. In this work, a procedure is
	described for reciprocal-space maximization of a likelihood function
	based on experimental phases and characteristics of the electron-density
	map. The procedure can readily be applied to phase improvement based
	on solvent flattening and can potentially incorporate information
	on a wide variety of other characteristics of the electron-density
	map.},
  keywords = {Bacterial Proteins, Computational Biology, Computer Simulation, Crystallography,
	Electrostatics, Likelihood Functions, Macromolecular Substances,
	Mathematical Computing, Models, Molecular, Multivariate Analysis,
	Non-P.H.S., Non-U.S. Gov't, P.H.S., Protein Conformation, Proteins,
	Reproducibility of Results, Research Support, Rhodococcus, Software,
	Solvents, Theoretical, U.S. Gov't, X-Ray, 10531484},
  pii = {GR0940},
}

@ARTICLE{Terwilliger2003,
  author = {Thomas C Terwilliger},
  title = {Automated main-chain model building by template matching and iterative
	fragment extension.},
  journal = {Acta Crystallogr D Biol Crystallogr},
  year = {2003},
  volume = {59},
  pages = {38-44},
  number = {Pt 1},
  month = {Jan},
  abstract = {An algorithm for the automated macromolecular model building of polypeptide
	backbones is described. The procedure is hierarchical. In the initial
	stages, many overlapping polypeptide fragments are built. In subsequent
	stages, the fragments are extended and then connected. Identification
	of the locations of helical and beta-strand regions is carried out
	by FFT-based template matching. Fragment libraries of helices and
	beta-strands from refined protein structures are then positioned
	at the potential locations of helices and strands and the longest
	segments that fit the electron-density map are chosen. The helices
	and strands are then extended using fragment libraries consisting
	of sequences three amino acids long derived from refined protein
	structures. The resulting segments of polypeptide chain are then
	connected by choosing those which overlap at two or more C(alpha)
	positions. The fully automated procedure has been implemented in
	RESOLVE and is capable of model building at resolutions as low as
	3.5 A. The algorithm is useful for building a preliminary main-chain
	model that can serve as a basis for refinement and side-chain addition.},
  keywords = {Algorithms, Automa, Automated, Chemical, Crystallography, Databases,
	Macromolecular Substances, Models, Molecular, P.H.S., Pattern Recognition,
	Peptide Fragments, Protein, Protein Structure, Research Support,
	S. Gov't, Secondary, Software, U., X-Ray, tion, 12499537},
  pii = {S0907444902018036},
}

@ARTICLE{terwillinger/eisenberg-87,
  author = {Thomas C. Terwilliger and David Eisenberg},
  title = {Isomorphous Replacement: Effects of Errors on the
	
	  Phase Probability Distribution},
  journal = ac,
  year = {1987},
  volume = {A43},
  pages = {6--13},
}

@ARTICLE{terwillinger/eisenberg-83,
  author = {Thomas C. Terwilliger and David Eisenberg},
  title = {Unbiased Three-Dimensional Refinement of Heavy-Atom
	
	  Parameters by Correlation of Origin-Removed Patterson Functions},
  journal = ac,
  year = {1983},
  volume = {A39},
  pages = {813--817},
  optnote = {heavy},
}

@ARTICLE{Thompson1997,
  author = {JD Thompson and TJ Gibson and F Plewniak and F Jeanmougin and DG
	Higgins},
  title = {The {CLUSTAL}_{X} windows interface: flexible strategies for multiple
	sequence alignment aided by quality analysis tools.},
  journal = {Nucleic Acids Res},
  year = {1997},
  volume = {25},
  pages = {4876-82},
  number = {24},
  month = {Dec},
  abstract = {CLUSTAL X is a new windows interface for the widely-used progressive
	multiple sequence alignment program CLUSTAL W. The new system is
	easy to use, providing an integrated system for performing multiple
	sequence and profile alignments and analysing the results. CLUSTAL
	X displays the sequence alignment in a window on the screen. A versatile
	sequence colouring scheme allows the user to highlight conserved
	features in the alignment. Pull-down menus provide all the options
	required for traditional multiple sequence and profile alignment.
	New features include: the ability to cut-and-paste sequences to change
	the order of the alignment, selection of a subset of the sequences
	to be realigned, and selection of a sub-range of the alignment to
	be realigned and inserted back into the original alignment. Alignment
	quality analysis can be performed and low-scoring segments or exceptional
	residues can be highlighted. Quality analysis and realignment of
	selected residue ranges provide the user with a powerful tool to
	improve and refine difficult alignments and to trap errors in input
	sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on
	Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows
	(32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.},
  keywords = {Algorithms, Amino Acid Sequence, Data Display, Molecular Sequence
	Data, Research Support, Non-U.S. Gov't, Sequence Alignment, Sequence
	Homology, Nucleic Acid, User-Computer Interface, 9396791},
  owner = {brooks},
  pdf = {Thompson_Higgins-The CLUSTAL_X_windows_interface_flexible strategies_for_multiple_sequence_alignment_aided_by_quality_analysis_tools.pdf},
  pii = {gka797},
}

@ARTICLE{trueblood:96,
  author = {Trueblood, K. N. and B\"{u}rgi, H. B. and Burzlaff, H. and
 Dunitz,
	J. D. and Gramaccioli, C. M. and Schulz,
 H. H. and Shmueli, U. and
	Abrahams, S. C.},
  title = {Atomic Displacement Parameter Nomenclature: Report of a
 Subcommittee
	on Atomic Displacement Parameter
 Nomenclature},
  journal = {Acta Cryst.},
  year = {1996},
  volume = {A52},
  pages = {770-781},
}

@ARTICLE{Vagin1997,
  author = {Vagin, A. and Teplyakov, A.},
  title = {{{\it MOLREP}: an Automated Program for Molecular Replacement}},
  journal = {Journal of Applied Crystallography},
  year = {1997},
  volume = {30},
  pages = {1022--1025},
  number = {6},
  month = {Dec},
  abstract = {MOLREP is an automated program for molecular replacement which utilizes
	effective new approaches in data processing and rotational and translational
	searching. These include an automatic choice of all parameters, scaling
	by Patterson origin peaks and soft resolution cut-off. One of the
	cornerstones of the program is an original full-symmetry translation
	function combined with a packing function. Information from the model
	already placed in the cell is incorporated in both translation and
	packing functions. A number of tests using experimental data proved
	the ability of the program to find the correct solution in difficult
	cases.},
  doi = {doi:10.1107/S0021889897006766},
  pdf = {Vagin1997.pdf},
  url = {http://scripts.iucr.org/cgi-bin/paper?li5010},
}

@ARTICLE{vaguine-etal-99,
  author = {A. A. Vaguine and J. Richelle and S. J. Wodak},
  journal = ac,
  year = {1999},
  volume = {D55},
  pages = {191-205},
}

@ARTICLE{Vriend1990,
  author = {G. Vriend},
  title = {W{HAT} {IF}: a molecular modeling and drug design program.},
  journal = {J Mol Graph},
  year = {1990},
  volume = {8},
  pages = {52-6, 29},
  number = {1},
  month = {Mar},
  abstract = {A FORTRAN 77 computer program has been written to aid with macromolecular
	modeling and drug design. Called WHAT IF, it provides an intelligent
	and flexible environment for displaying, manipulating, and analyzing
	small molecules, proteins, nucleic acids, and their interactions.
	A relational protein structure database is incorporated to be queried.
	The program is suitable for most common crystallographic work. The
	menu-driven operation of WHAT IF, combined with the use of default
	values wherever user input is required, makes it very easy to use
	for a novice user while keeping full flexibility for more sophisticated
	studies. Although there are not too many unique features in WHAT
	IF, the fact that everything is integrated in one program makes it
	a unique tool for many purposes.},
  keywords = {Amino Acid, Amino Acid Sequence, Animals, Carboxypeptidase B, Carboxypeptidases,
	Carboxypeptidases A, Cattle, Cell Surface, Comparative Study, Computer
	Graphics, Crystallography, Databases, Drug Design, Factual, GTP-Binding
	Proteins, Humans, Lysine Carboxypeptidase, Magnetic Resonance Spectroscopy,
	Models, Molecular, Molecular Sequence Data, Molecular Weight, Non-U.S.
	Gov't, Protein Conformation, Protein Structure, Receptors, Research
	Support, Secondary, Sequence Alignment, Sequence Homology, Signal
	Transduction, Software, Statistical, Statistics, Substrate Specificity,
	X-Ray, 2268628},
}

@ARTICLE{Vriend1993,
  author = {Gert Vriend and Chris Sander},
  title = {Quality control of protein models: Directional atomic contact analysis.},
  journal = {J.Appl.Cryst},
  year = {1993},
  volume = {26},
  pages = {47-60},
}

@ARTICLE{waasmaier:95,
  author = {Waasmaier, D. and Kirfel, A.},
  title = {New Analytical Scattering-Factor Functions for Free Atoms
 and Ions},
  journal = {Acta Cryst.},
  year = {1995},
  volume = {A51},
  pages = {416-431},
}

@ARTICLE{wang-81,
  author = {B. C. Wang},
  journal = ac,
  year = {1981},
  volume = {A37},
  pages = {Suppl. {C}--11},
  optnote = {abstract only},
}

@ARTICLE{weinzierl-etal-69,
  author = {J. E. Weinzierl and D. Eisenberg and R. E. Dickerson},
  journal = ac,
  year = {1969},
  volume = {B25},
  pages = {380},
}

@ARTICLE{wilson:00,
  author = {Wilson, M. A. and Br\"{u}nger, A. T.},
  title = {The 1.0{{\AA}} Crystal Structure of {C}a$^{2+}$-bound
 Calmodulin:
	an Analysis of Disorder and Implications
 for Functionally Relevant
	Plasticity},
  journal = {JMB},
  year = {2000},
  volume = {301},
  pages = {1237-1256},
  number = {5},
}

@ARTICLE{woolfson/yao-94,
  author = {M. M. Woolfon and Jia--Xing Yao},
  title = {On the Application of One-Wavelength Anomalous Scattering.
	
	   {IV} The Absolute Configuration of the Anomalous Scatterers.},
  journal = ac,
  year = {1994},
  volume = {D50},
  pages = {7--10},
}

@ARTICLE{wright-77,
  author = {Wright, C. S.},
  journal = jmb,
  year = {1977},
  volume = {111},
  pages = {439--457},
  optnote = {referenced by mlphare},
}

@ARTICLE{yonath-etal-86,
  author = {A. Yonath and M. A. Saper and F. Frolow and I.
	
	  Makowsky and H. G. Wittman},
  title = {Characterisation of Single Crystals of the Large
	
	  Ribosomal Particles from a Mutant of {\em Bacillus
	
	  stearothermophilus}},
  journal = jmb,
  year = {1986},
  volume = {192},
  pages = {161--162},
}

@ARTICLE{zhang/main-90,
  author = {Zhang, K. Y. J. and Main, P.},
  journal = ac,
  year = {1990},
  volume = {A46},
  pages = {377--381},
  optnote = {squash (/dm)},
}

@BOOK{zlotnik-91,
  title = {The {POSIX.1} Standard: A Programmer's Guide},
  publisher = {Benjamin/Cummings},
  year = {1991},
  author = {Fred Zlotnik},
  optnote = {ISBN 0805396055},
}

@ARTICLE{Zvelebil1987,
  author = {MJ Zvelebil and GJ Barton and WR Taylor and MJ Sternberg},
  title = {Prediction of protein secondary structure and active sites using
	the alignment of homologous sequences.},
  journal = {J Mol Biol},
  year = {1987},
  volume = {195},
  pages = {957-61},
  number = {4},
  month = {Jun},
  abstract = {The prediction of protein secondary structure (alpha-helices, beta-sheets
	and coil) is improved by 9\% to 66\% using the information available
	from a family of homologous sequences. The approach is based both
	on averaging the Garnier et al. (1978) secondary structure propensities
	for aligned residues and on the observation that insertions and high
	sequence variability tend to occur in loop regions between secondary
	structures. Accordingly, an algorithm first aligns a family of sequences
	and a value for the extent of sequence conservation at each position
	is obtained. This value modifies a Garnier et al. prediction on the
	averaged sequence to yield the improved prediction. In addition,
	from the sequence conservation and the predicted secondary structure,
	many active site regions of enzymes can be located (26 out of 43)
	with limited over-prediction (8 extra). The entire algorithm is fully
	automatic and is applicable to all structural classes of globular
	proteins.},
  keywords = {Algorithms, Amino Acid Sequence, Binding Sites, Protein Conformation,
	Research Support, Non-U.S. Gov't, 3656439},
  owner = {brooks},
}

@ARTICLE{brunger-95,
  author = {{A.~T. Br\"unger}},
  title = {The free {$R$} Value: A More Objective Statistic for Crystallography},
  journal = {Methods in Enzym.},
  year = {1995},
  optnote = {In press. \texttt{http:/\slash xplor.csb.yale.edu\slash group\slash
	papers\slash meth\char`\_enz\char`\_rfree\slash meth\char`\_enz\char`\_rfree\char`\_www.html}},
}

@MANUAL{fortran-77,
  title = {American National Standard Programming Language {FORTRAN}},
  author = {{ANSI}},
  organization = {American National Standards Institute, Inc},
  year = {1978},
  optnote = {{ANSI X3.9--1978, ISO 1539--1980 (E)\@.
	
			    \texttt{http:/\slash www.fortran.com\slash
	
			  fortran\slash rjcnf0001.html}}},
}

@ARTICLE{ccp4-94,
  author = {{Collaborative Computational Project, Number 4}},
  title = {The {CCP4} Suite: Programs for Protein Crystallography},
  journal = ac,
  year = {1994},
  volume = {D50},
  pages = {760--763},
}

@MANUAL{mil-std-78,
  title = {Military Standard, {Fortran}, {DOD} Supplement to
	
	  American Standard X3.9--1978, {MIL--STD--1793}},
  author = {{DOD}},
  organization = {{US Government Printing Office}},
  year = {1978},
}

@ARTICLE{skarzynski-92,
  author = {{Tadeusz Skar\dot{z}y\'{n}ski}},
  title = {Crystal Structure of $\alpha$-Dendrotoxin from the
	
	  Green Mamba Venom and its Comparison with the Structure of Bovine
	
	  Pancreatic Trypsin Inhibitor},
  journal = jmb,
  year = {1992},
  volume = {224},
  pages = {671--683},
  optnote = {toxd example (1dtx)},
}

@PROCEEDINGS{study-w/e-88,
  title = {Improving Protein Phases},
  year = {1988},
  editor = {S. Bailey and E. Dodson and S. Phillips},
  number = {DL/SCI/R26, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{study-w/e-94,
  title = {From First Map to Final Model},
  year = {1994},
  editor = {S. Bailey and R. Hubbard and D. Waller},
  number = {DL/SCI/R35, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{study-w/e-92,
  title = {Molecular Replacement},
  year = {1992},
  editor = {E. J. Dodson and S. Gover and W. Wolf},
  number = {DL/SCI/R33, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{study-w/e-96,
  title = {Macromolecular Refinement},
  year = {1996},
  editor = {E. J. Dodson and M. Moore and S. Bailey},
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{cc6,
  title = {Crystallographic Computing 6: A Window on Modern Crystallography},
  year = {1993},
  editor = {H. D. Flack and L. P\'ark\'anyi and K. Simon},
  series = {IUCr Crystallographic Symposia},
  publisher = {Oxford University Press},
  organization = {IUCr},
  optnote = {ISBN 0--19--855788--4},
}

@PROCEEDINGS{study-w/e-89,
  title = {Molecular Simulation and Protein Crystallography},
  year = {1989},
  editor = {J. Goodfellow and K. Henrick and R. Hubbard},
  number = {DL/SCI/R27, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@BOOK{int-tab-a,
  title = {International Tables for Crystallography},
  publisher = {Kluwer},
  year = {1992},
  editor = {Theo Hahn},
  volume = {A},
  edition = {third},
}

@PROCEEDINGS{study-w/e-87,
  title = {Computational Aspects of Protein Crystal Data Analysis},
  year = {1987},
  editor = {J. R. Helliwell and P. A. Machin and M. Z. Papiz},
  number = {DL/SCI/R25, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{study-w/e-90,
  title = {Accuracy and Reliability of Macromolecular Structures},
  year = {1990},
  editor = {K. Henrick and D. S. Moss and I. J. Tickle},
  number = {DL/SCI/R28, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{study-w/e-95,
  title = {Making the Most of your Model},
  year = {1995},
  editor = {W. N. Hunter and J. M. Thornton and S. Bailey},
  number = {DL-CONF-95-001, ISSN 1358--6254},
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{study-w/e-85,
  title = {Molecular Replacement},
  year = {1985},
  editor = {P. A. Machin},
  number = {DL/SCI/R23, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{study-w/e-80,
  title = {Refinement of Protein Structures},
  year = {1980},
  editor = {P. A. Machin and J. W. Campbell and M. Elder},
  number = {DL/SCI/R16, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{cc5,
  title = {Crystallographic Computing 5: From Chemistry to Biology},
  year = {1991},
  editor = {D. Moras and A. D. Podjarny and J. C. Thierry},
  series = {IUCr Crystallographic Symposia},
  publisher = {Oxford University Press},
  organization = {IUCr},
  optnote = {ISBN 0--19--855384--6},
}

@BOOK{jargon,
  title = {The New Hacker's Dictionary},
  publisher = {{MIT} Press},
  year = {1993},
  editor = {Eric Raymond},
  edition = {Second},
  optnote = {ISBN 0--262--68079--3.  Available online as the
	
	  {`Jargon File'}.  {\tt http://www.ccil.org\slash jargon\slash jargon.html}.},
}

@PROCEEDINGS{study-w/e-93,
  title = {Data Collection and Processing},
  year = {1993},
  editor = {L. Sawyer and N. Isaacs and S. Bailey},
  number = {DL/SCI/R34, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@PROCEEDINGS{study-w/e-91,
  title = {Isomorphous Replacement and Anomalous Scattering},
  year = {1991},
  editor = {W. Wolf and P. R. Evans and A. G. W. Leslie},
  number = {DL/SCI/R32, } # swissn,
  series = {{CCP4} {D}aresbury Study Weekend},
  address = dladdr,
  publisher = dlab,
  organization = dlab,
  key = {CCP4},
}

@BOOK{wyckoff-85a,
  title = {Diffraction Methods for Biological Macromolecules},
  publisher = {Academic Press},
  year = {1985},
  editor = {H. Wyckoff and C. H. W. Hirs and S. N. Timasheff},
  volume = {114},
  series = {Methods in Enzymology},
  optnote = {crystallisation, data collection},
}

@BOOK{wyckoff-85b,
  title = {Diffraction Methods for Biological Macromolecules},
  publisher = {Academic Press},
  year = {1985},
  editor = {H. Wyckoff and C. H. W. Hirs and S. N. Timasheff},
  volume = {115},
  series = {Methods in Enzymology},
}

@MISC{skewing,
  title = {The Joy of Skewing},
  howpublished = {CCP4 documentation},
  key = {CCP4},
  optnote = {Documentation for Bricogne's molecular averaging
	
	  program package},
}