Nucleic Acids Research, 2000, Vol. 28, No. 1 235-242
© 2000 Oxford University Press
The Protein Data Bank
1Research Collaboratory for Structural Bioinformatics (RCSB), 2Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, 3National Institute of Standards and Technology, Route 270, Quince Orchard Road, Gaithersburg, MD 20899, USA, 4San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA, 5Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0500, USA and 6The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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.
* To whom correspondence should be addressed at: Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA. Tel: +1 732 445 4667; Fax: +1 732 445 4320; Email: berman@rcsb.rutgers.edu
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W.-Y. Chu, Y.-F. Huang, C.-C. Huang, Y.-S. Cheng, C.-K. Huang, and Y.-J. Oyang ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors Nucleic Acids Res., July 1, 2009; 37(suppl_2): W396 - W401. [Abstract] [Full Text] [PDF]
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 E. D. Kouri, N. E. Labrou, S. D. Garbis, K. I. Kalliampakou, C. Stedel, M. Dimou, M. K. Udvardi, P. Katinakis, and E. Flemetakis Molecular and Biochemical Characterization of the Parvulin-Type PPIases in Lotus japonicus Plant Physiology, July 1, 2009; 150(3): 1160 - 1173. [Abstract] [Full Text] [PDF]
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P. V. Burra, Y. Zhang, A. Godzik, and B. Stec Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure PNAS, June 30, 2009; 106(26): 10505 - 10510. [Abstract] [Full Text] [PDF]
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G. Moroy, E. Martin, A. Dejaegere, and R. H. Stote Molecular Basis for Bcl-2 Homology 3 Domain Recognition in the Bcl-2 Protein Family: IDENTIFICATION OF CONSERVED HOT SPOT INTERACTIONS J. Biol. Chem., June 26, 2009; 284(26): 17499 - 17511. [Abstract] [Full Text] [PDF]
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O. Fornes, R. Aragues, J. Espadaler, M. A. Marti-Renom, A. Sali, and B. Oliva ModLink+: improving fold recognition by using protein-protein interactions Bioinformatics, June 15, 2009; 25(12): 1506 - 1512. [Abstract] [Full Text] [PDF]
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S. Lee and T. L Blundell BIPA: a database for protein-nucleic acid interaction in 3D structures Bioinformatics, June 15, 2009; 25(12): 1559 - 1560. [Abstract] [Full Text] [PDF]
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R. V. Spriggs, Y. Murakami, H. Nakamura, and S. Jones Protein function annotation from sequence: prediction of residues interacting with RNA Bioinformatics, June 15, 2009; 25(12): 1492 - 1497. [Abstract] [Full Text] [PDF]
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F. Khatib, C. A. Rohl, and K. Karplus Pokefind: a novel topological filter for use with protein structure prediction Bioinformatics, June 15, 2009; 25(12): i281 - i288. [Abstract] [Full Text] [PDF]
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I. Wallach and R. H. Lilien Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation Bioinformatics, June 15, 2009; 25(12): i296 - i304. [Abstract] [Full Text] [PDF]
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L. Xie, L. Xie, and P. E. Bourne A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery Bioinformatics, June 15, 2009; 25(12): i305 - i312. [Abstract] [Full Text] [PDF]
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I. Derler, M. Fahrner, O. Carugo, M. Muik, J. Bergsmann, R. Schindl, I. Frischauf, S. Eshaghi, and C. Romanin Increased Hydrophobicity at the N Terminus/Membrane Interface Impairs Gating of the Severe Combined Immunodeficiency-related ORAI1 Mutant J. Biol. Chem., June 5, 2009; 284(23): 15903 - 15915. [Abstract] [Full Text] [PDF]
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 P. T. Lang, S. R. Brozell, S. Mukherjee, E. F. Pettersen, E. C. Meng, V. Thomas, R. C. Rizzo, D. A. Case, T. L. James, and I. D. Kuntz DOCK 6: Combining techniques to model RNA-small molecule complexes RNA, June 1, 2009; 15(6): 1219 - 1230. [Abstract] [Full Text] [PDF]
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J. Ashworth and D. Baker Assessment of the optimization of affinity and specificity at protein-DNA interfaces Nucleic Acids Res., June 1, 2009; 37(10): e73 - e73. [Abstract] [Full Text] [PDF]
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S. Mukherjee and Y. Zhang MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming Nucleic Acids Res., June 1, 2009; 37(11): e83 - e83. [Abstract] [Full Text] [PDF]
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C. Hsiao and L. D. Williams A recurrent magnesium-binding motif provides a framework for the ribosomal peptidyl transferase center Nucleic Acids Res., June 1, 2009; 37(10): 3134 - 3142. [Abstract] [Full Text] [PDF]
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L. J. Gourlay, I. Santi, A. Pezzicoli, G. Grandi, M. Soriani, and M. Bolognesi Group B Streptococcus Pullulanase Crystal Structures in the Context of a Novel Strategy for Vaccine Development J. Bacteriol., June 1, 2009; 191(11): 3544 - 3552. [Abstract] [Full Text] [PDF]
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J.-F. Wang, K. Gong, D.-Q. Wei, Y.-X. Li, and K.-C. Chou Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one Protein Eng. Des. Sel., June 1, 2009; 22(6): 349 - 355. [Abstract] [Full Text] [PDF]
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