The Protein Data Bank

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1999 Dec 11

PMID 10592235

Citations 13033

Authors

H M Berman

J Westbrook

Z Feng

G Gilliland

T N Bhat

H Weissig

I N Shindyalov

P E Bourne

Affiliations

Soon will be listed here.

Abstract

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

Citing Articles

Network pharmacology and experimental analysis reveal Ethyl caffeate delays osimertinib resistance in lung cancer by suppression of MET.

Sang S, Han Y, Zhou H, Kang X, Gong Y Cancer Cell Int. 2025; 25(1):99.

PMID: 40089772 DOI: 10.1186/s12935-025-03690-5.

High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells.

Rega C, Tsitsa I, Roumeliotis T, Krystkowiak I, Portillo M, Yu L Nat Commun. 2025; 16(1):2579.

PMID: 40089461 DOI: 10.1038/s41467-025-57537-8.

Integrating artificial intelligence in drug discovery and early drug development: a transformative approach.

Ocana A, Pandiella A, Privat C, Bravo I, Luengo-Oroz M, Amir E Biomark Res. 2025; 13(1):45.

PMID: 40087789 DOI: 10.1186/s40364-025-00758-2.

Sporophyte-directed gametogenesis in Arabidopsis.

Sivakumar P, Pandey S, Ramesha A, Davda J, Singh A, Kumar C Nat Plants. 2025; .

PMID: 40087543 DOI: 10.1038/s41477-025-01932-y.

Integrated virtual screening and compound generation targeting H275Y mutation in the neuraminidase gene of oseltamivir-resistant influenza strains.

Khan W, Khan N, Tembhre M, Malik Z, Ansari M, Mishra A Mol Divers. 2025; .

PMID: 40085404 DOI: 10.1007/s11030-025-11163-0.

References

Quinn G, Wang H, Martinez D, Bourne P . Developing protein documentaries and other multimedia presentations for molecular biology. Pac Symp Biocomput. 1999; :380-91. DOI: 10.1142/9789814447300_0037. View

Bernstein F, Koetzle T, Williams G, Meyer Jr E, Brice M, Rodgers J . The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977; 112(3):535-42. DOI: 10.1016/s0022-2836(77)80200-3. View

Kabsch W, Sander C . Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983; 22(12):2577-637. DOI: 10.1002/bip.360221211. View

Hogue C, Ohkawa H, BRYANT S . A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database. Trends Biochem Sci. 1996; 21(6):226-9. View

Nayal M, Hitz B, Honig B . GRASS: a server for the graphical representation and analysis of structures. Protein Sci. 1999; 8(3):676-9. PMC: 2144291. DOI: 10.1110/ps.8.3.676. View

Orengo C, Michie A, Jones S, Jones D, Swindells M, Thornton J . CATH--a hierarchic classification of protein domain structures. Structure. 1997; 5(8):1093-108. DOI: 10.1016/s0969-2126(97)00260-8. View

Gibrat J, Madej T, BRYANT S . Surprising similarities in structure comparison. Curr Opin Struct Biol. 1996; 6(3):377-85. DOI: 10.1016/s0959-440x(96)80058-3. View

Murzin A, Brenner S, Hubbard T, Chothia C . SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995; 247(4):536-40. DOI: 10.1006/jmbi.1995.0159. View

Lee B, Richards F . The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971; 55(3):379-400. DOI: 10.1016/0022-2836(71)90324-x. View

10.

Berman H, Olson W, Beveridge D, Westbrook J, Gelbin A, Demeny T . The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 1992; 63(3):751-9. PMC: 1262208. DOI: 10.1016/S0006-3495(92)81649-1. View

11.

Suhnel J . Image library of biological macromolecules. Comput Appl Biosci. 1996; 12(3):227-9. DOI: 10.1093/bioinformatics/12.3.227. View

12.

Vaguine A, RICHELLE J, Wodak S . SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr. 1999; 55(Pt 1):191-205. DOI: 10.1107/S0907444998006684. View

13.

Bourne P, Berman H, McMahon B, Watenpaugh K, Westbrook J, Fitzgerald P . Macromolecular Crystallographic Information File. Methods Enzymol. 1997; 277:571-90. DOI: 10.1016/s0076-6879(97)77032-0. View

14.

Pearson W, Lipman D . Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988; 85(8):2444-8. PMC: 280013. DOI: 10.1073/pnas.85.8.2444. View

15.

Laskowski R, Hutchinson E, Michie A, Wallace A, Jones M, Thornton J . PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends Biochem Sci. 1998; 22(12):488-90. DOI: 10.1016/s0968-0004(97)01140-7. View

16.

Ulrich E, Markley J, Kyogoku Y . Creation of a nuclear magnetic resonance data repository and literature database. Protein Seq Data Anal. 1989; 2(1):23-37. View

17.

Westhead D, Slidel T, Flores T, Thornton J . Protein structural topology: Automated analysis and diagrammatic representation. Protein Sci. 1999; 8(4):897-904. PMC: 2144300. DOI: 10.1110/ps.8.4.897. View

18.

Shindyalov I, Bourne P . Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 1998; 11(9):739-47. DOI: 10.1093/protein/11.9.739. View

19.

Quinn G, Taylor A, Wang H, Bourne P . Development of Internet-based multimedia applications. Trends Biochem Sci. 1999; 24(8):321-4. DOI: 10.1016/s0968-0004(99)01434-6. View

20.

Holm L, Sander C . Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 1998; 26(1):316-9. PMC: 147193. DOI: 10.1093/nar/26.1.316. View