This file was created with JabRef 1.8b2. Encoding: ISO8859_1 @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}, }