@techreport{ADSC:97, key = "Quantum 4", title =" Quantum 4R Specifications", type = "web page", note="http://www.adsc-xray.com/Q4techspecs.html", institution="Area Detector Systems Corporation", City="Poway. CA", year=1997 } @article{Allen_et_al:73, author = "F. H. Allen and O. Kennard and W. D. S. Motherwell and W. G. Town and D. G. Watson", title = "Cambridge Crystallographic Data Centre. II. Structural Data File", journal = "J. Chem. Doc.", volume = "13", pages = "119 -- 123", year = 1973} @book{Aho_et_al:87, author = "Alfred V. Aho and John E. Hopcroft and Jeffrey D. Ullman", title = "Data Structures and Algorithms", series = "Computer Science and Information Processing", publisher = "Addison-Wesley", City = "Reading, MA", year = 1987 } @article{Andrews:87, author = "Nancy Andrews", title = "Rich Text Format Standard Makes Transferring Text Easier ", journal = "Microsoft Systems Journal", volume = "2", pages = "63 -- 67", year = 1987 } @inBook{Berman_Westbrook:03, key="Ch. 4.X", editor="S. R. Hall and B. McMahon", author = "Helen M. Berman and John D. Westbrook", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="4.X MACROMOLECULAR EXCHANGE DICTIONARY (pdbx)", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @inBook{Bernstein:03, key="Ch. 3.7", editor="S. R. Hall and B. McMahon", author = "H. J. Bernstein", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="3.7. Classification and use of image data", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @techreport{Bernstein:97a, author = "Herbert J. Bernstein", title = "cif2cif -- CIF Copy Program", institution = "Bernstein + Sons", type = "software", note = "included in http://www.bernstein-plus-sons.com/software/ciftbx", year = 1997} @conference{Bernstein_Bernstein:96, author="F. C. Bernstein and H. J. Bernstein", title="Translating mmCIF Data into PDB Entries", organization="IUCr", institution="IUCr", location="Seattle, WA", note="presented at CIF workshop at Seattle IUCr meeting, 7-17 August 1996. Software available at http://www.bernstein-plus-sons.com/software/cif2pdb", year = 1996 } @conference{Bernstein_Bernstein:02, author= "H. J. Bernstein and F. C. Bernstein", title = "Yaxdf and the Interaction between CIF and XML", organization = "XIX Congress and General Assembly of the International Union of Crystallography", location = "Geneva, Switzerland", month= "August", year = "2002", journal = "Acta Cryst.", volume = "A58 (Supplement)", pages = "C257" } @article{Bernstein_Bernstein_Bourne:98, author="H. J. Bernstein and F. C. Bernstein and P. E. Bourne", title="CIF Applications. VIII. pdb2cif: Translating PDB Entries into mmCIF Format", journal="J. Appl. Cryst.", note="Software available at http://www.bernstein-plus-sons.com/software/pdb2cif", volume="31", pages="282 -- 295", year=1998 } @inBook{Bernstein_Ellis:03, key="Ch. 5.6", editor="S. R. Hall and B. McMahon", author = "P. J. Ellis and H. J. Bernstein", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="5.6. CBFlib: an ANSI C library for manipulating image data", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @inBook{Bernstein_Hall:03, key="Ch. 5.4", editor="S. R. Hall and B. McMahon", author = "H. J. Bernstein and P. R. Hall", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="5.4 CIFTBX: Fortran tools for manipulating CIFs", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @article{Bernstein_Hall:98, author="H. J. Bernstein and S. R. Hall", title="CIF Applications. VII CYCLOPS2: Extending the Validation of CIF Data Names", journal="J. Appl. Cryst.", note="Software available at http://www.bernstein-plus-sons.com/software/ciftbx/cyclops.src", volume="31", pages="278 -- 281", year=1998 } @inBook{Bernstein_Hammersley:03, key="Ch. 2.3", editor="S. R. Hall and B. McMahon", author = "H. J. Bernstein and A. P. Hammersley", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="2.3. Specification of the Crystallographic Binary File (imgCIF/CBF)", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @article{Bernstein_et_al:77, author= "F. C. Bernstein and T. F. Koetzle and G. J. B. Williams and E. F. {Meyer, Jr.} and M. D. Brice and J. R. Rodgers and O. Kennard and T. Shimanouchi and M. Tasumi", title = "The Protein Data Bank: a computer-based archival file for macromolecular structures", journal = "J. Mol. Biol.", volume = "112", pages = "535 -- 542", year=1977 } @article{Bourne_Berman_McMahon_Watenpaugh_Westbrook_Fitzgerald:97, author="P. E. Bourne and H. M. Berman and B. McMahon and K. D. Watenpaugh and J. Westbrook and P. M. D. Fitzgerald", title="The Macromolecular Crystallographic Information File (mmCIF)", journal="Methods in Enzymology", volume="277", pages="571 -- 590", year=1997 } @techreport{Bray_Paoli_Sperberg-McQueen:98, author="T. Bray and J. Paoli and C.M. Sperberg-McQueen", key="Bray, Paoli, Sperberg-McQueen", title="Extensible Markup Language (XML)", type = "web page", note="W3C Recommendation 10-Feb-98, REC-xml-19980210, http://www.w3.org/TR/1998/REC-xml-19980210", institution="W3C", year=1998 } @techreport{Bray_et_al:98, author="T. Bray and J. Paoli and C.M. Sperberg-McQueen", key="Bray, Paoli, Sperberg-McQueen", title="Extensible Markup Language (XML)", type = "web page", note="W3C Recommendation 10-Feb-98, REC-xml-19980210, http://www.w3.org/TR/1998/REC-xml-19980210", institution="W3C", year=1998 } @book{CSDUM:78, key = "CSD", title = "Cambridge Crystallographic Database User Manual", publisher = "Crystallographic Data Centre", city = "Cambridge, England", month = "April", year = "1978" } @article{Diamond:71, key = "diamond", author = "R. Diamond", title = "A real-space refinement procedure for proteins", journal = "Acta Cryst.", volume = "A27", pages = "436 -- 452", year = 1971, } @book{Dubuisson:00, author="Olivier Dubuisson", title="ASN.1 Communication between Heterogeneous Systems", note="translated from French by Phillipe Fouquart", publisher = "Morgan Kaufmann", city = "San Francisco", year = "2000", pages = "562" } @inBook{Fitzgerald_et_al:03a, key="Ch. 3.6", editor="S. R. Hall and B. McMahon", author = "P. M. D. Fitzgerald and J. D. Westbrook and P. E. Bourne and B. McMahon and K. D. Watenpaugh and H. M. Berman", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="3.6. Classification and use of macromolecular data", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @inBook{Fitzgerald_et_al:03b, key="Ch. 4.5", editor="S. R. Hall and B. McMahon", author = "P. M. D. Fitzgerald and J. D. Westbrook and P. E. Bourne and B. McMahon and K. D. Watenpaugh and H. M. Berman", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="4.5. Macromolecular dictionary (mmCIF)", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @article{Flack_Blanc_Schwarzenbach:1992, author = "H. D. Flack and E. Blanc and D. Schwarzenbach", journal = "J. Appl. Cryst.", year = "1992", volume = "25", pages = "455 -- 459" } @techreport{Freed_Borenstein:96a, author = "N. Freed and N. Borenstein", title = "Multipurpose Internet Mail Extensions (MIME) Part One: Format of Internet Message Bodies", institution = "Internet Engineering Task Force", type = "RFC", number = "2045", note = "http://www.ietf.org/rfc/rfc2045.txt", year = 1996 } @techreport{Freed_Borenstein:96b, author = "N. Freed and N. Borenstein", title = "Multipurpose Internet Mail Extensions (MIME) Part Two: Media Types", institution = "Internet Engineering Task Force", type = "RFC", number = "2046", note = "http://www.ietf.org/rfc/rfc2046.txt", year = 1996 } @techreport{Freed_Klensin_Postel:96, author = "N. Freed and J. Klensin and J. Postel", title = "Multipurpose Internet Mail Extensions (MIME) Part Four: Registration Procedures", institution = "Internet Engineering Task Force", type = "RFC", number = "2048", note = "http://www.ietf.org/rfc/rfc2048.txt", year = 1996 } @techreport{Freed_Borenstein:96c, author = "N. Freed and N. Borenstein", title = "Multipurpose Internet Mail Extensions (MIME) Part Five: Conformance Criteria and Examples", institution = "Internet Engineering Task Force", type = "RFC", number = "2049", note="http://www.ietf.org/rfc/rfc2049.txt", year = 1996 } @article{Hall_Allen_Brown:91, author = "S. R. Hall and F. H. Allen and I. D. Brown", title = "The Crystallographic Information File (CIF): a New Standard Archive File. for Crystallography", journal = "Acta Cryst.", volume = "A47", pages = "655 -- 685", year = 1991 } @article{Hall:91, author="S. R. Hall", title="The STAR File: A New Format for Electronic Data Transfer and Archiving", journal= "J. Chem. Inform. Comp. Sci.", volume="31", pages="326 -- 333", year=1991 } @article{Hall:93a, author="S. R. Hall", title="CIF Appl. II. CIFIO: for CIF Input/Output in the Xtal System", journal="J. Appl. Cryst.", volume="26", pages="474 -- 479", year=1993 } @article{Hall:93b, author="S. R. Hall", title="CIF Appl. III. CYCLOPS: for validating CIF Data Names", journal="J. Appl. Cryst.", volume="26", pages="480 -- 481", year=1993 } @article{Hall:93c, author="S. R. Hall", title="CIF Appl. IV. CIFtbx: A Toolbox for Manipulating CIF's", journal="J. Appl. Cryst.", volume="26", pages="482 -- 494", year=1993 } @article{Hall_Bernstein:96, author="S. R. Hall and H. J. Bernstein", title="CIF Applications. CIFtbx2: Extended Tool Box for Manipulating CIFs", journal="J. Appl. Cryst.", volume="29", pages="598--603", year=1996 } @inBook{Hall_McMahon:03, key="Ch. 1.1", editor="S. R. Hall and B. McMahon", author = "S. R. Hall and B. McMahon", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="1.1. Genesis of the Crystallographic Information File", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @inBook{Hall_Westbrook:03, key="Ch. 2.2", editor="S. R. Hall and B. McMahon", author = "S. R. Hall and J. D. Westbrook", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="2.2. Specification of the Crystallographic Information File", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @techreport{Hall_King_Stewart:95, author="S. R. Hall and G. D. S. King and J. M. Stewart", title="Xtal 3.4 Users Manual. Report", type = "manual", institution="University of Western Australia", year=1995 } @article{Hall_Cook:95, author="S. R. Hall and A. P. F. Cook", title="Data Definition Language for STAR File Dictionaries", journal="J. Chem. Inform. Comp. Sci.", volume="R35", page="819 -- 825", year=1995 } @article{Hall_Sievers:93, author = "S. R. Hall and R. Sievers", title= "CIF applications. I. QUASAR: for extracting data from a CIF", journal = "J. Appl. Cryst.", volume = "26", pages = "469 -- 473", year= 1993 } @article{Hall_Spadaccini:94, author="S. R. Hall and N. Spadaccini", title="The STAR File: Detailed Specifications", journal="J. Chem. Inform. Comp. Sci.", volume="34", pages="505 -- 508", year=1994 } @techreport{Hammersley:97, author = "A. P. Hammersley", title = "FIT2D: An Introduction and Overview", institution = "ESRF", type = "ESRF Internal Report", number = "ESRF97HA02T", year = 1997 } @inBook{Hammersley_Bernstein_Westbrook:03, key="Ch. 4.6", editor="S. R. Hall and B. McMahon", author = "A. P. Hammersley and H. J. Bernstein and J. D. Westbrook", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="4.6. Image dictionary (imgCIF)", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @article{Heller_Milne_Feldmann:77, author = "S. R. Heller and G. W. A. Milne and R. J. Feldmann", title = "A computer-based chemical information system", journal = "Science", volume = "195", pages = "253 -- 259", year = 1977 } @article{Hester_Okamura:98, author = "J. R. Hester and F. P. Okamura", journal = "J. Appl. Cryst.", year = "1998", volume = "31", pages = "965 -- 968", title = "CIF Applications. X. Automatic Construction of CIF Input Functions: CifSieve" } @techreport{HTML:89, author = "T. Berners-Lee", title = "Information management: A proposal", type = "proposal", year = "1989", month = "March", institution = "CERN", note = "see http://www.w3.org/History/1989/proposal.html"} @techreport{IEEE:85, key="IEEE", title = "IEEE Standard for Binary Floating--Point Arithmetic", type="ANSI/IEEE Std", number="754--1985", institution="Institute of Electrical and Electronics Engineers, Inc.", author = "IEEE", city="NY", year=1985} @techreport{Johnson:75, author = "S. C. Johnson", title = "YACC: Yet another Compiler-Compiler", note = "also in UNIX Programmer's Manual, Supplementary Documents, 4.2 Berkeley Software Distribution, Virtual VAX-11 Version, March 1984", type = "manual", number = "32", year = "1975", institution = "Bell Laboratories", location = "Murray Hill, NJ", } @techreport{Lesk_Schmidt:75, author = "M. E. Lesk and E. Schmidt", title = "Lex - A Lexical Analyzer Generator", note = "also in UNIX Programmer's Manual, Supplementary Documents, 4.2 Berkeley Software Distribution, Virtual VAX-11 Version, March 1984", type = "manual", number = "39", year = "1975", institution = "Bell Laboratories", location = "Murray Hill, NJ", } @techreport{Keller:96, author="P. A. Keller", title="A mmCIF Toolbox for CCP4 Applications", type="workshop presentation", organization="IUCr", institution="IUCr", location="Seattle, WA", note="CIF workshop at Seattle IUCr meeting, 7-17 August 1996. abstract E0726", year = 1996 } @article{Klosowski_et_al:97, author = "P. Klosowski and M. Koennecke and J. Z. Tischler and R. Osborn", title="NeXus: A common format for the exchange of neutron and synchrotron data", journal = "Physica B: Condensed Matter", volume = "B 241-243", pages = "151 -- 153", year = 1997 } @book{Knuth:84, author = "Donald E. Knuth", title = "The \TeX Book", year = "1984", publisher = "Addison-Wesley", pages = 483, city = "Reading, Mass."} @book{Lycos:75, title="Computer Networking and Chemistry", editor="Peter Lykos", series = "ACS Symposium Series", volume = 19, publisher = "American Chemical Society", city = "Washington", pages = 237, year = 1975 } @techreport{MAR:97, key="MAR 345", title="The mar345 Image Plate Detector", type = "web page", note="http://www.marresearch.com/ip.htm", institution="MAR Research", city="Norderstedt, Germany", year=1997 } @inBook{McMahon:03, key="Ch. 5.3", editor="S. R. Hall and B. McMahon", author = "B. McMahon", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="5.3. Syntactic utilities for CIF", publisher="Kluwer Academic Publishers", city="Dordrecht", year=2004 } @article{Moffat_Bell_Witten:97, author="A. Moffat and T. C. Bell and I. H. Witten", title = "Lossless compression for text and images", journal = "International Journal of High Speed Electronics and Systems", volume = "8", pages = "179 -- 231", year = 1997 } @techreport{Moore:96, author = "K. Moore", title = "MIME (Multipurpose Internet Mail Extensions) Part Three: Message Header Extensions for Non-ASCII Text", institution = "Internet Engineering Task Force", type = "RFC", number = "2047", note = "http://www.ietf.org/rfc/rfc2047.txt.", year = 1996 } @article{Murray-Rust_Rzepa:99, author="P. Murray-Rust and H. Rzepa", title= "Chemical markup, XML and the WWW, Part I: Basic principles", journal = "J. Chem. Inf . Comp. Sci", volume = "39", number = "6", pages="928 -- 942", year = 1999 } @techreport{NCSA:93, author = "NCSA", title = "NCSA HDF: Specification and Developer's Guide", type = "manual", institution = "University of Illinois at Urbana-Champaign", note = " Version 3.2", year = 1993 } @article{Ohkawa_Ostell_Bryant:95, author = "H. Ohkawa and J. Ostell and S. Bryant", year = "1995", title = "{MMDB}: An {ASN.1} specification for macromolecular structure", journal = "ISMB", volume = "3", pages = "259 -- 267" } @techreport{Rivest:92, author = "R. Rivest", title = "The MD5 Message-Digest Algorithm", institution = "Internet Engineering Task Force", type = "RFC", number = "1321", note="http://www.ietf.org/rfc/rfc1321.txt", year = 1992 } @book{PDB_newsletter_1:74, key = "PDB Newsletter 1", year = 1974, title = "{PDB Newsletter}", month = "September", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 20} @book{PDB_newsletter_2:76, key = "PDB Newsletter 2", year = 1976, title = "{PDB Newsletter}", month = "March", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 4} @book{PDB_newsletter_3:76, key = "PDB Newsletter 3", year = 1976, title = "{PDB Newsletter}", month = "November", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 6} @book{PDB_newsletter_4:77, key = "PDB Newsletter 4", year = 1977, title = "{PDB Newsletter}", month = "May", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 8} @book{PDB_newsletter_5:77, key = "PDB Newsletter 5", year = 1977, title = "{PDB Newsletter}", month = "November", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 6} @book{PDB_newsletter_10:79, key = "PDB Newsletter 10", year = 1979, title = "{PDB Newsletter}", month = "October", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 6} @book{PDB_newsletter_37:86, key = "PDB Newsletter 37", year = 1986, title = "{PDB Newsletter}", month = "July", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 6} @book{PDB_newsletter_44:88, key = "PDB Newsletter 44", year = 1988, title = "{PDB Newsletter}", month = "April", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 6} @book{PDB_newsletter_46:88, key = "PDB Newsletter 46", year = 1988, title = "{PDB Newsletter}", month = "October", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 6} @book{PDB_newsletter_47:89, key = "PDB Newsletter 47", year = 1989, title = "{PDB Newsletter}", month = "January", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 8} @book{PDB_newsletter_48:89, key = "PDB Newsletter 48", year = 1989, title = "{PDB Newsletter}", month = "April", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 8} @book{PDB_newsletter_50:89, key = "PDB Newsletter 50", year = 1989, title = "{PDB Newsletter}", month = "October", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 8} @book{PDB_newsletter_51:90, key = "PDB Newsletter 51", year = 1990, title = "{PDB Newsletter}", month = "January", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 8} @book{PDB_newsletter_53:90, key = "PDB Newsletter 53", year = 1990, title = "{PDB Newsletter}", month = "July", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 9} @book{PDB_newsletter_55:91, key = "PDB Newsletter 55", year = 1991, title = "{PDB Newsletter}", month = "January", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 10} @book{PDB_newsletter_59:92, key = "PDB Newsletter 59", year = 1992, title = "{PDB Newsletter}", month = "January", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 37} @book{PDB_newsletter_67:94, key = "PDB Newsletter 67", year = 1994, title = "{PDB Newsletter}", month = "January", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 28} @book{PDB_newsletter_69:94, key = "PDB Newsletter 69", year = 1994, title = "{PDB Newsletter}", month = "July", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 22} @book{PDB_newsletter_70:94, key = "PDB Newsletter 70", year = 1994, title = "{PDB Newsletter}", month = "October", institution = "Brookhaven National Laboratory", publisher = "Brookhaven National Laboratory", city = "Upton, NY", pages = 11} @article{Spadaccini_Hall:94, author="N. Spadaccini and S. R. Hall", title="Star_Base: Accessing STAR File Data", journal="J. Chem. Inform. Comp. Sci.", volume="34", pages="509 -- 516", year=1994 } @techreport{Stampf:94, author = "D. R. Stampf", title = "ZINC -- Galvanizing CIF to work with UNIX", type = "manual", institution = "Protein Data Bank, Brookhaven National Laboratory", city = "Upton, NY", year = "1994" } @techreport{SGML:86, key = "SGML", title= "International Standard ISO 8879 Information Processing - Text and Office Systems - Standardized Generalized Markup Language (SGML), First Edition", type = "standard", year = "1986", note = "1986-10-15 UDC 681.3.06 Ref. No. ISO 8879-1986(E)", institution = "International Organization for Standardization"} @techreport{Tosic_Westbrook:98, author = "O. Tosic and J. D. Westbrook", title="CIFPARSE: A Library of Access Tools for mmCIF, Reference Guide", type = "manual", number="Version 3.01", note="http://pdb.rutgers.edu/mmcif/CIFPARSE/cifparse/cifparse.html", institution="Nucleic Acid Database Project, Dept. of Chemistry, Rutgers, The State University of NJ", year=1998 } @techreport{Walters_Stahl:94, author = "P. Walters and M. Stahl", title = "BABEL Reference Manual", type = "manual", institution = "Dolata Research Group, Department of Chemistry, University of Arizona", note = "Version 1.06", year = 1994} @inBook{Westbrook:03, key="Ch. 5.5", editor="S. R. Hall and B. McMahon", author = "John D. Westbrook", series="International Tables For Crystallography", title="Volume G: Definition and Exchange of Crystallographic Data", chapter="5.5. Tools for manipulating macromolecular data", publisher="Kluwer Academic Publishers", City="Dordrecht", year=2004 } @techreport{Westbrook_Hall:95, author="J. Westbrook and S. R. Hall", title = "A Dictionary Description Language for Macromolecular Structure, Draft DDL V 2.1.0", note="http://www.iucr.org/iucr-top/cif/ddl/index.html", type = "manual", institution="IUCr COMCIFS", city="Dordrecht", year = 1995 } @article{Westbrook_Hsieh_Fitzgerald:97, author="J. D. Westbrook and S.-H. Hsieh and P. M. D. Fitzgerald", title = "CIFLIB: An Application Program Interface to CIF Dictionaries and Data Files", journal = "J. Appl. Cryst.", volume = "30", pages = "79 -- 83", year = 1997 } @techreport{X.680:94, key = "X.680", title = "Information technology - Abstract Syntax Notation One (ASN.1): Specification of basic notation", type = "ITU standard", institution = "International Telecommunications Union", year = 1994} @article{Orengo_et_al:97, author="C. A. Orengo and A. D. Michie and S. Jones and D. T. Jones and M. B. Swindells and J. M. Thornton", year = 1997, title = "CATH- A Hierarchic Classification of Protein Domain Structures", journal = "Structure", volume = "5", number = "8", pages = "1093 -- 1108" } @article{Pearl_et_al:00, author = "F. M. G. Pearl and D. Lee and J. E. Bray and I. Sillitoe and A. E. Todd and A. P. Harrison and J. M. Thornton and C. A. Orengo", year = "2000", title = "Assigning genomic sequences to CATH", journal = "Nucleic Acids Research", volume = "28", number = "1", pages = "277 -- 282"} @book{Valiela:01, author = "I. Valiela", title = "Doing Science: Design, Analysis and Communication of Scientific Research", publisher = "Oxford University Press", city = "New York", year = "2001", pages = "294 + vii"} @article{Holm_Sander:96, author = "L. Holm and C. Sander", title = "The {FSSP} database: fold classification based on structure-structure alignment of proteins", journal = "Nucleic Acids Research", volume = "24", year = "1996", pages = "206 -- 210" } @article{Holm_Sander:94, author = "L. Holm and C. Sander", title = "The {FSSP} database of structurally aligned protein fold families", journal = "Nucleic Acids Research", volume = "22", year = "1994", pages = "3600 -- 3609" } @article{Hendlich:98, author = "M. Hendlich", title = "Databases for protein-ligand complexes", journal = "Acta Cryst.", volume = "D54", year = "1998", pages = "1178 -- 1182" } @article{Codd:70, author = "E. F. Codd", title = "A Relational Model of Data for Large Shared Data Banks", journal = "Communications of the ACM", volume = "13", number = "6", month = "June", year = "1970", pages = "377 -- 387" } @article{Berman_et_al:00, author = "H. M. Berman and J. Westbrook and Z. Feng and G. Gilliland and T. N. Bhat and H. Weissig and I. N. Shindyalov and P. E. Bourne", title= "The Protein Data Bank", journal = "Nucleic Acids Research", volume = "28", pages = "235 -- 242", year = "2000" } @article{Berman_et_al:92, author = "H. M. Berman and W. K. Olson and D. L. Beveridge and J. Westbrook and A. Gelbin and T. Demeny and S.-H. Hsieh and A. R. Srinivasan and B. Schneider", title = "The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids", journal = "Biophys. J.", volume = "63", pages = "751 -- 759", year = "1992"} @book{NDB_newsletter_1:91, key = "NDB Newsletter 1", year = 1991, title = "{Nucleic Acid DataBase Newsletter}", month = "December", institution = "Rutgers, the State University of New Jersey", publisher = "Rutgers, the State University of New Jersey", city = "Piscataway, NJ", pages = 20} @inBook{Burley_Bonanno:03, key="Ch. 29", author = "S. K. Burley and J. B. Bonanno", title="Structural Bioinformatics / edited by P. E. Bourne, H. Weissig", chapter="29. Structural Genomics", publisher="Wiley-Liss", city="Hoboken, NJ", pages = "591 -- 612", year=2004 } @article{Elias_et_al:56, author = "P. Elias and A. Feinstein and C. E. Shannon", title = "A Note on the Maximum Flow Through a Network", journal = "IRE Transactions on Information Theory (later IEEE Transactions on Information Theory)", volume = "IT-2", month = "December", pages = "117 -- 199", year = "1956" } @article{Ford_Fulkerson:56, author = "L. R. Ford and D. R. Fulkerson", title = "Maximal Flow through a Network", journal = "Canadian Journal of Mathematics", volume = "8", pages = "399 -- 404", year = 1956 } @article{Lin_et_al:00, author= "D. Lin and N. O. Manning and J. Jiang and E. E. Abola and D. Stampf and J. Prilusky and J. L. Sussman", title = "{AutoDep}: A web based system for deposition and validation of macromolecular structural information", journal = "Acta Cryst.", volume = "D56", pages = "828 -- 841", year = "2000" } @inbook{Bernstein_et_al:74, author = "H. J. Bernstein and L. C. Andrews and H. M. Berman and F. C. Bernstein and G. H. Campbell and H. L. Carrell and H. B. Chiang and W. C. Hamilton and D. D. Jones and D. Klunk and T. F. Koetzle and E. F. Meyer Jr. and C. N. Morimoto and S. Sevian and R. K. Stodola and M. M. Strongson and T. V. Willoughby", chapter = "{CRYSNET} -- A Network of Intelligent Remote Graphics Terminals", title = "Second Annual AEC Scientific Computer Information Exchange Meeting, Proceedings of the Technical Program", year = "1974", pages = "149 -- 161", note = "Brookhaven National Laboratory Report \#18803."} @article{Andrews_Bernstein:79, author = "L. C. Andrews and H. J. Bernstein", title = "The {NIH-EPA} Chemical Information System", journal = "ONLINE", month = "March", year = "1979", pages = "35 -- 49"} @article{Bairoch_Apweiler:00, author = "A. Bairoch and R. Apweiler", title = "The {Swiss-Prot} protein sequence data bank and its supplement {TrEMBL} in 2000", journal = "Nucleic Acids Research", volume = "28", pages = "45 -- 48", year = "2000" } @article{Wu_et_al:03, author = "C. H. Wu and L.-S. L. Yeh and H. Huang and L. Arminski and J. Castro-Alvear and Y. Chen and Z.-Z. Hu and R. S. Ledley and P. Kourtesis and B. E. Suzek and C. R. Vinayaka and J. Zhang and W. C. Barker", title = "The Protein Information Resource", journal = "Nucleic Acids Research", volume ="31", pages = "345 -- 347", year = "2003" } @article{Sigrist_et_al:02, author = "C. J. Sigrist and L. Cerutti and N. Hulo and A. Gattiker and L. Falquet and M. Pagni and A. Bairoch and P. Bucher", title = "{PROSITE}: a documented database using patterns and profiles as motif descriptors", journal = "Brief Bioinform.", volume = "3", pages = "265 -- 274", year = "2002" } @article{Benson_et_al:03, author = "D. A. Benson and I. Karsch-Mizrachi and D. J. Lipman and J. Ostell and D. L. Wheeler", title = "{GenBank}", journal = "Nucleic Acids Research", volume = "31", pages = "23 -- 27", year = "2003" } @inBook{Talbot_Cuticchia:99, author = "C. C. Talbot Jr. and A. J. Cuticchia", chapter = "1.13. Human mapping databases", title = "Current protocols in human genetics", editor = "N. C. Dracopoli and J. Haines and B. R. Korf and C. Morton and C. E. Seidman and J. G. Seidman", city = "New York", publisher = "John Wiley and Sons", pages = "1.13.1 -- 1.13.12", year = "1999" } @article{Stoesser_et_al:03, author = "W. Baker and A. van den Broek and M. Garcia-Pastor and C. Kanz and T. Kulikova and R. Leinonen and Q. Lin and V. Lombard and R. Lopez and R. Mancuso and F. Nardone and P. Stoehr and M. A. Tuli and K. Tzouvara and R. Vaughan ", title="The {EMBL} Nucleotide Sequence Database: major new developments", journal = "Nucleic Acids Research", volume = "31", number = "1", pages = "17 -- 22", year = "2003" } @article{Henikoff_et_al:00, author = "J. G. Henikoff and E. A. Greene and S. Pietrokovski and S. Henikoff", title = "Increased coverage of protein families with the {Blocks} Database servers", journal = "Nucleic Acids Research", volume = "28", number = "1", pages = "228 -- 230", year = "2000" } @article{Henrick:98, author = "K. Henrick", title = "{PQS}: a protein quaternary structure file server", journal = "Trends in Biochemical Sciences", volume = "23", number = "9", pages = "358 -- 361", year = "1998" } @article {Seavey_et_al:91, title = "A Relational Database for Sequence-Specific Protein {NMR} Data", author = "B.R. Seavey and E.A. Farr and W.M. Westler and J.L. Markley", journal = "J. Biomol. NMR", volume = "1", pages = "217 -- 236", year = "1991" } @article{Gilliland_et_al:94, author = "G. L. Gilliland and M. Tung and D. M. Blakeslee and J. Ladner", title = "The Biological Macromolecule Crystallization Database, Version 3.0: New Features, Data, and the {NASA} Archive for Protein Crystal Growth Data", journal = "Acta Crystallogr.", volume = "D50", pages = "408 -- 413", year = "1994" } @article{Hendlich_et_al:03, title = "Relibase - Design and Development of a Database for Comprehensive Analysis of Protein-Ligand Interactions", author = "M. Hendlich and A. Bergner and J. Gunther and G. Klebe", journal = "J. Mol. Biol.", volume = "326", pages = "607 -- 620", year = "2003" } @article{Murzin_et_al:95, author = "A. G. Murzin and S. E. Brenner and T. Hubbard and C. Chothia", title = "{SCOP}: a structural classification of proteins database for the investigation of sequences and structures", journal = "J. Mol. Biol.", volume = "247", pages = "536 -- 540", year = "1995" } @article{Lo_Conte_et_al:02, author = "L. Lo Conte and S. E. Brenner and T. J. P. Hubbard and C. Chothia and A. Murzin", title = "{SCOP} database in 2002: refinements accommodate structural genomics", journal = "Nucleic Acids Research", volume = "30", number = "1", pages = "264 -- 267", year = 2002 } @misc{fn1, key = " 1", year = "...", note= "See {http://www.ccdc.cam.ac.uk/about/history.html}"} @misc{fn2, key = "000ccdc_request", note= "See {http://www.ccdc.cam.ac.uk/products/csd/request/index.html}"} @misc{fn3, key = "000ebi_about", note= "See {http://www.ebi.ac.uk/Information/About\_EBI/about\_ebi.html\#ab\_1\_his}"} @misc{fn4, key = "000pdbj", note= "See {http://pdbj.protein.osaka-u.ac.jp/NPPSFA/index.html}"} @misc{fn5, key = "000rcsb_2003q3", note= "See {http://www.rcsb.org/pdb/newsletter/2003q3/new\_features.html}"} @misc{fn6, key = "000bmrb", note= "See {http://www.bmrb.wisc.edu}"} @misc{fn7, key = "000rcsb_database", note= "See {http://www.rcsb.org/pdb/links.html\#Databases}"} @misc{fn8, key = "000ebi_services", note= "See {http://www.ebi.ac.uk/services/index.html}"} @misc{fn9, key = "000ncbi", note= "See {http://www.ncbi.nlm.nih.gov:80/gquery/gquery.fcgi}"} @misc{fn10, key = "000google", note= "See {{\it e.g.} http://www.google.com}"} @misc{fn11, key = "000ebi_dali", note= "See {http://www.ebi.ac.uk/dali/}"} @misc{fn12, key = "000ncbi_entrez", note= "See {http://www.ncbi.nlm.nih.gov/Entrez}"} @misc{fn13, key = "000ncbi_mmdb", note= "See {http://www.ncbi.nlm.nih.gov:80/Structure/MMDB/mmdb.shtml}"} @misc{fn14, key = "000mrc-lmb_scop", note= "See {http://scop.mrc-lmb.cam.ac.uk/scop/}"} @misc{fn15, key = "000ucl_cath", note= "See {http://www.biochem.ucl.ac.uk/bsm/cath/}"} @misc{fn17, key = "000wwwpdb", note= "See {http://www.wwpdb.org/wwpdb\_charter.html}"} @misc{fn18, key = "000relibase", note= "See {http://relibase.ccdc.cam.ac.uk}"} @misc{fn19, key = "000rcsb_2003q2_sf", note= "See {http://www.rcsb.org/pdb/newsletter/2003q2/sf\_data.html}"} @misc{fn20, key = "000bmc_update", note= "See {http://fsrv1.bmc.uu.se/eds/eds\_update.html}"} @misc{fn21, key = "zzzmirror", note = "Please note that the concept of a mirror site predates the existence of the world wide web, and can be applied to ftp sites, gopher holes, databases, web sites and many other on-line data compendia."} @misc{fn22, key = "000rcsb_uniformity", note = "See {http://www.rcsb.org/pdb/uniformity/}"} @article{Mondragon_Harrison:91, author = "A. Mondragon and S. C. Harrison", title = "The phage 434 {Cro/OR1} complex at 2.5 {A} resolution", journal = "J. Mol. Biol.", volume = "219", number = "2", pages = "321 -- 334", year = "1991", note = "PDB entry 3CRO 29 July 1990"} } @article{Teeter:84, title = "Water Structure of a Hydrophobic Protein at Atomic Resolution. Pentagon Rings of Water Molecules in Crystals of Crambin", author = "M. M. Teeter", journal = "Proc.Nat.Acad.Sci. USA", volume = "81", year = "1984", pages = "6014 -- 6018" } @misc{Hendrickson_Teeter:81, author= " W. A. Hendrickson and M. M. Teeter", note = "PDB Entry {1CRN}, 30 April 1981" } @misc{Dayhoff_et_al:65, key = "dayhoff_a", author = "M. O. Dayhoff and R. V. Eck and M. A. Chang and M. R. Sochard", title = "Atlas of Protein Sequence and Structure, Vol. 1", publisher = "National Biomedical Research Foundation", city = "Silver Spring, MD", pages = "93", year = 1965} @misc{Dayhoff_et_al:78, key = "dayhoff_b", author = "M. O. Dayhoff (editor) and L. T. Hunt and W. C. Barker and R. M. Schwartz and B. C. Orcutt and C. L. Young", title = "Atlas of Protein Sequence and Structure, Vol 5", publisher = "National Biomedical Research Foundation", city = "Silver Spring, MD", pages = "470", year = 1978}