International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F. ch. 24.5, pp. 675-684   | 1 | 2 |
https://doi.org/10.1107/97809553602060000722

Chapter 24.5. The Protein Data Bank, 1999–

H. M. Berman,a* J. Westbrook,a Z. Feng,a G. Gilliland,b T. N. Bhat,b H. Weissig,c I. N. Shindyalovc and P. E. Bourned

a Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA,bNational Institute of Standards and Technology, Biotechnology Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA,cSan Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA, and dDepartment of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA
Correspondence e-mail:  berman@rcsb.rutgers.edu

References

First citation Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S. H., Srinivasan, A. R. & Schneider, B. (1992). The Nucleic Acid Database – a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751–759.Google Scholar
First citation Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235–242.Google Scholar
First citation Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. E., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.Google Scholar
First citation Bourne, P., Berman, H. M., Watenpaugh, K., Westbrook, J. D. & Fitzgerald, P. M. D. (1997). The macromolecular Crystallographic Information File (mmCIF). Methods Enzymol. 277, 571–590.Google Scholar
First citation Brookhaven National Laboratory (1998). AutoDep. Version 2.1. Brookhaven National Laboratory, Upton, NY, USA.Google Scholar
First citation Dodge, C., Schneider, R. & Sander, C. (1998). The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Res. 26, 313–315.Google Scholar
First citation Feng, Z., Hsieh, S.-H., Gelbin, A. & Westbrook, J. (1998). MAXIT: macromolecular exchange and input tool. NDB-120. Rutgers University, New Brunswick, NJ, USA.Google Scholar
First citation Feng, Z., Westbrook, J. & Berman, H. M. (1998). NUCheck. NDB-407. Rutgers University, New Brunswick, NJ, USA.Google Scholar
First citation Gibrat, J.-F., Madej, T. & Bryant, S. H. (1996). Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6, 377–385.Google Scholar
First citation Gilliland, G. L. (1988). A Biological Macromolecule Crystallization Database: a basis for a crystallization strategy. J. Cryst. Growth, 90, 51–59.Google Scholar
First citation Hogue, C. W., Ohkawa, H. & Bryant, S. H. (1996). A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends Biochem. Sci. 21, 226–229.Google Scholar
First citation Holm, L. & Sander, C. (1998). Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26, 316–319.Google Scholar
First citation Hooft, R. W. W., Sander, C. & Vriend, G. (1996). Verification of protein structures: side-chain planarity. J. Appl. Cryst. 29, 714–716.Google Scholar
First citation Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577–2637.Google Scholar
First citation Laskowski, R. A., Hutchinson, E. G., Michie, A. D., Wallace, A. C., Jones, M. L. & Thornton, J. M. (1997). PDBsum: a web-based database of summaries and analyses of all PDB structures. Trends Biochem. Sci. 22, 488–490.Google Scholar
First citation Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291.Google Scholar
First citation Laskowski, R. A. & Wallace, A. C. (1998). Enzyme Structures Database. http://www.biochem.ucl.ac.uk/bsm/enzymes/ .Google Scholar
First citation Lee, B. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400.Google Scholar
First citation Markley, J. L., Bax, A., Arata, Y., Hilbers, C. W., Kaptein, R., Sykes, B. D., Wright, P. E. & Wüthrich, K. (1998). Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC–IUBMB–IUPAB Inter-Union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. J. Biomol. Nucl. Magn. Reson. 12, 1–23.Google Scholar
First citation Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536–540.Google Scholar
First citation National Library of Medicine (1989). MEDLINE [database online]. Bethesday, MD, USA. Updated weekly. Available from: National Library of Medicine; OVID, Murray, UT; The Dialog Corporation, Palo Alto, CA.Google Scholar
First citation Nayal, M., Hitz, B. C. & Honig, B. (1999). GRASS: a server for the graphical representation and analysis of structures. Protein Sci. 8, 676–679.Google Scholar
First citation Neshich, G., Togawa, R., Vilella, W. & Honig, B. (1998). STING (Sequence To and withIN Graphics) PDB_Viewer. Protein Data Bank Q. Newsl. 85, 6–7.Google Scholar
First citation Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. (1997). CATH – a hierarchic classification of protein domain structures. Structure, 5, 1093–1108.Google Scholar
First citation Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 24, 2444–2448.Google Scholar
First citation Quinn, G., Taylor, A., Wang, H.-P. & Bourne, P. E. (1999). Development of internet-based multimedia applications. Trends Biochem. Sci. 24, 321–324.Google Scholar
First citation Quinn, G., Wang, H.-P., Martinez, D. & Bourne, P. E. (1999). Developing protein documentaries and other multimedia presentations for molecular biology. In Pacific symposium on biocomputing, edited by R. Altman, K. Dunker, L. Hunter, T. Klein & K. Lauderdale, pp. 380–391. Singapore.Google Scholar
First citation Shindyalov, I. N. & Bourne, P. E. (1997). Protein data representation and query using optimized data decomposition. Comput. Appl. Biosci. 13, 487–496.Google Scholar
First citation Shindyalov, I. N. & Bourne, P. E. (1998). Protein structure alignment by incremental combinatorial extension of the optimum path. Protein Eng. 11, 739–747.Google Scholar
First citation Siddiqui, A. & Barton, G. (1996). Perspectives on protein engineering 1996, Vol. 2, CD-ROM edition, edited by M. J. Geisow. BIODIGM Ltd (UK). ISBN 0–9529015-0–1.Google Scholar
First citation Sühnel, J. (1996). Image library of biological macromolecules. Comput. Appl. Biosci. 12, 227–229.Google Scholar
First citation Sybase Inc. (1995). 70202–01–1100–01 SYBASE SQL server release 11.0. Emeryville, CA, USA.Google Scholar
First citation Ulrich, E. L., Markley, J. L. & Kyogoku, Y. (1989). Creation of a nuclear magnetic resonance data repository and literature database. Protein Seq. Data Anal. 2, 23–37.Google Scholar
First citation Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Cryst. D55, 191–205.Google Scholar
First citation Weissig, H., Shindyalov, I. N. & Bourne, P. E. (1998). Macromolecular structure databases: past progress and future challenges. Acta Cryst. D54, 1085–1094.Google Scholar
First citation Westbrook, J., Feng, Z. & Berman, H. M. (1998). ADIT – the AutoDep Input Tool. RCSB-99. Department of Chemistry, Rutgers, The State University of New Jersey, USA.Google Scholar
First citation Westhead, D., Slidel, T., Flores, T. & Thornton, J. (1998). Protein structural topology: automated analysis and diagrammatic representation. Protein Sci. 8, 897–904.Google Scholar