Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (435K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (5894)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Berman, H. M.
Right arrow Articles by Bourne, P. E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Berman, H. M.
Right arrow Articles by Bourne, P. E.
Social Bookmarking
 Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2000, Vol. 28, No. 1 235-242
© 2000 Oxford University Press

The Protein Data Bank

Helen M. Berman1,2,*, John Westbrook1,2, Zukang Feng1,2, Gary Gilliland1,3, T. N. Bhat1,3, Helge Weissig1,4, Ilya N. Shindyalov4 and Philip E. Bourne1,4,5,6

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
J. Biol. Chem.Home page
K.-J. Kim, M. C. Park, S. J. Choi, Y. S. Oh, E.-C. Choi, H. J. Cho, M. H. Kim, S.-H. Kim, D. W. Kim, S. Kim, et al.
Determination of Three-dimensional Structure and Residues of the Novel Tumor Suppressor AIMP3/p18 Required for the Interaction with ATM
J. Biol. Chem., May 16, 2008; 283(20): 14032 - 14040.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
S. Meshinchi, D. L. Stirewalt, T. A. Alonzo, T. J. Boggon, R. B. Gerbing, J. L. Rocnik, B. J. Lange, D. G. Gilliland, and J. P. Radich
Structural and numerical variation of FLT3/ITD in pediatric AML
Blood, May 15, 2008; 111(10): 4930 - 4933.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
C. Cole, J. D. Barber, and G. J. Barton
The Jpred 3 secondary structure prediction server
Nucleic Acids Res., May 7, 2008; (2008) gkn238v1.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
R. Mosca and T. R. Schneider
RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes
Nucleic Acids Res., May 6, 2008; (2008) gkn197v1.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
A. Alfieri, E. Malito, R. Orru, M. W. Fraaije, and A. Mattevi
Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase
PNAS, May 6, 2008; 105(18): 6572 - 6577.
[Abstract] [Full Text] [PDF]


Home page
Brief BioinformHome page
S. J. Sammut, R. D. Finn, and A. Bateman
Pfam 10 years on: 10 000 families and still growing
Brief Bioinform, May 1, 2008; 9(3): 210 - 219.
[Abstract] [Full Text] [PDF]


Home page
J. Clin. Endocrinol. Metab.Home page
R. Menassa, V. Tardy, F. Despert, C. Bouvattier-Morel, J. P. Brossier, M. Cartigny, and Y. Morel
p.H62L, a Rare Mutation of the CYP21 Gene Identified in Two Forms of 21-Hydroxylase Deficiency
J. Clin. Endocrinol. Metab., May 1, 2008; 93(5): 1901 - 1908.
[Abstract] [Full Text] [PDF]


Home page
Protein Eng Des SelHome page
Y.-R. Tang, Z.-Y. Sheng, Y.-Z. Chen, and Z. Zhang
An improved prediction of catalytic residues in enzyme structures
Protein Eng. Des. Sel., May 1, 2008; 21(5): 295 - 302.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
V. I. Lesk and M. J. E. Sternberg
3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
Bioinformatics, May 1, 2008; 24(9): 1137 - 1144.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
C. X. Weichenberger, P. Byzia, and M. J. Sippl
Visualization of unfavorable interactions in protein folds
Bioinformatics, May 1, 2008; 24(9): 1206 - 1207.
[Abstract] [Full Text] [PDF]


Home page
Biophys. JHome page
O. N. Yogurtcu, S. B. Erdemli, R. Nussinov, M. Turkay, and O. Keskin
Restricted Mobility of Conserved Residues in Protein-Protein Interfaces in Molecular Simulations
Biophys. J., May 1, 2008; 94(9): 3475 - 3485.
[Abstract] [Full Text] [PDF]


Home page
HypertensionHome page
J. A. Hernandez Prada, A. J. Ferreira, M. J. Katovich, V. Shenoy, Y. Qi, R. A.S. Santos, R. K. Castellano, A. J. Lampkins, V. Gubala, D. A. Ostrov, et al.
Structure-Based Identification of Small-Molecule Angiotensin-Converting Enzyme 2 Activators as Novel Antihypertensive Agents
Hypertension, May 1, 2008; 51(5): 1312 - 1317.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
S. Lyskov and J. J. Gray
The RosettaDock server for local protein-protein docking
Nucleic Acids Res., April 28, 2008; (2008) gkn216v1.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
E. Mashiach, D. Schneidman-Duhovny, N. Andrusier, R. Nussinov, and H. J. Wolfson
FireDock: a web server for fast interaction refinement in molecular docking
Nucleic Acids Res., April 19, 2008; (2008) gkn186v1.
[Abstract] [Full Text] [PDF]


Home page
Biophys. JHome page
L. Wroblewska, A. Jagielska, and J. Skolnick
Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models
Biophys. J., April 15, 2008; 94(8): 3227 - 3240.
[Abstract] [Full Text] [PDF]


Home page
Protein Eng Des SelHome page
D. A.C. Beck, A. L. Jonsson, R. D. Schaeffer, K. A. Scott, R. Day, R. D. Toofanny, D. O.V. Alonso, and V. Daggett
Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
Protein Eng. Des. Sel., April 14, 2008; (2008) gzn011v1.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
H. G. Hocking, A. P. Herbert, D. Kavanagh, D. C. Soares, V. P. Ferreira, M. K. Pangburn, D. Uhrin, and P. N. Barlow
Structure of the N-terminal Region of Complement Factor H and Conformational Implications of Disease-linked Sequence Variations
J. Biol. Chem., April 4, 2008; 283(14): 9475 - 9487.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
J. Esguerra, J. Warringer, and A. Blomberg
Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping
RNA, April 1, 2008; 14(4): 649 - 656.
[Abstract] [Full Text] [PDF]


Home page
Biophys. JHome page
M. Esmann, N. U. Fedosova, and D. Marsh
Osmotic Stress and Viscous Retardation of the Na,K-ATPase Ion Pump
Biophys. J., April 1, 2008; 94(7): 2767 - 2776.
[Abstract] [Full Text] [PDF]


Home page
Mol. Pharmacol.Home page
R. P. Riek, A. A. Finch, G. E. Begg, and R. M. Graham
Wide Turn Diversity in Protein Transmembrane Helices Implications for G-Protein-Coupled Receptor and Other Polytopic Membrane Protein Structure and Function
Mol. Pharmacol., April 1, 2008; 73(4): 1092 - 1104.
[Abstract] [Full Text] [PDF]


Home page
Mol. Biol. CellHome page
M. K. Singh, D. Dadke, E. Nicolas, I. G. Serebriiskii, S. Apostolou, A. Canutescu, B. L. Egleston, and E. A. Golemis
A Novel Cas Family Member, HEPL, Regulates FAK and Cell Spreading
Mol. Biol. Cell, April 1, 2008; 19(4): 1627 - 1636.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
S. Soro, A. Orecchia, L. Morbidelli, P. M. Lacal, V. Morea, K. Ballmer-Hofer, F. Ruffini, M. Ziche, S. D'Atri, G. Zambruno, et al.
A proangiogenic peptide derived from vascular endothelial growth factor receptor-1 acts through {alpha}5{beta}1 integrin
Blood, April 1, 2008; 111(7): 3479 - 3488.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
Y. Araiso, S. Palioura, R. Ishitani, R. L. Sherrer, P. O'Donoghue, J. Yuan, H. Oshikane, N. Domae, J. DeFranco, D. Soll, et al.
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation
Nucleic Acids Res., March 27, 2008; 36(4): 1187 - 1199.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
M. R. Gryk and J. C. Hoch
Local knowledge helps determine protein structures
PNAS, March 25, 2008; 105(12): 4533 - 4534.
[Full Text] [PDF]


Home page
BioinformaticsHome page
M. J. Sippl, S. J. Suhrer, M. Gruber, and M. Wiederstein
A discrete view on fold space
Bioinformatics, March 15, 2008; 24(6): 870 - 871.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
A. Biegert and J. Soding
De novo identification of highly diverged protein repeats by probabilistic consistency
Bioinformatics, March 15, 2008; 24(6): 807 - 814.
[Abstract] [Full Text] [PDF]


Home page
Proc. Natl. Acad. Sci. USAHome page
H. Gong and G. D. Rose
Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model
PNAS, March 4, 2008; 105(9): 3321 - 3326.
[Abstract] [Full Text] [PDF]


Home page
MicrobiologyHome page
M. T. Edwards, N. K. Fry, and T. G. Harrison
Clonal population structure of Legionella pneumophila inferred from allelic profiling
Microbiology, March 1, 2008; 154(3): 852 - 864.
[Abstract] [Full Text] [PDF]


Home page
Protein Eng Des SelHome page
C. D. Geierhaas, X. Salvatella, J. Clarke, and M. Vendruscolo
Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values
Protein Eng. Des. Sel., March 1, 2008; 21(3): 215 - 222.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
J. S. Richardson, B. Schneider, L. W. Murray, G. J. Kapral, R. M. Immormino, J. J. Headd, D. C. Richardson, D. Ham, E. Hershkovits, L. D. Williams, et al.
RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
RNA, March 1, 2008; 14(3): 465 - 481.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
S. Smit, K. Rother, J. Heringa, and R. Knight
From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal
RNA, March 1, 2008; 14(3): 410 - 416.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
Y. C. Chen and C. Lim
Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry
Nucleic Acids Res., March 1, 2008; 36(5): e29 - e29.
[Abstract] [Full Text] [PDF]


Home page
Antimicrob. Agents Chemother.Home page
F. Bos and J. Pleiss
Conserved Water Molecules Stabilize the {Omega}-Loop in Class A {beta}-Lactamases
Antimicrob. Agents Chemother., March 1, 2008; 52(3): 1072 - 1079.
[Abstract] [Full Text] [PDF]


Home page
GlycobiologyHome page
D. Shaya, B.-S. Hahn, T. M. Bjerkan, W. S. Kim, N. Y. Park, J.-S. Sim, Y.-S. Kim, and M. Cygler
Composite active site of chondroitin lyase ABC accepting both epimers of uronic acid
Glycobiology, March 1, 2008; 18(3): 270 - 277.
[Abstract] [Full Text] [PDF]


Home page
Mol. Pharmacol.Home page
R. Kondru, J. Zhang, C. Ji, T. Mirzadegan, D. Rotstein, S. Sankuratri, and M. Dioszegi
Molecular Interactions of CCR5 with Major Classes of Small-Molecule Anti-HIV CCR5 Antagonists
Mol. Pharmacol., March 1, 2008; 73(3): 789 - 800.
[Abstract] [Full Text] [PDF]


Home page
Biophys. JHome page
L. Celik, B. Schiott, and E. Tajkhorshid
Substrate Binding and Formation of an Occluded State in the Leucine Transporter
Biophys. J., March 1, 2008; 94(5): 1600 - 1612.
[Abstract] [Full Text] [PDF]


Home page
GeneticsHome page
J. F. Storz, F. G. Hoffmann, J. C. Opazo, and H. Moriyama
Adaptive Functional Divergence Among Triplicated {alpha}-Globin Genes in Rodents
Genetics, March 1, 2008; 178(3): 1623 - 1638.
[Abstract] [Full Text] [PDF]


Home page
J. Biol. Chem.Home page
L. E. Olesen, M. G. J. Ford, E. M. Schmid, Y. Vallis, M. M. Babu, P. H. Li, I. G. Mills, H. T. McMahon, and G. J. K. Praefcke
Solitary and Repetitive Binding Motifs for the AP2 Complex {alpha}-Appendage in Amphiphysin and Other Accessory Proteins
J. Biol. Chem., February 22, 2008; 283(8): 5099 - 5109.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
A. Randall, J. Cheng, M. Sweredoski, and P. Baldi
TMBpro: secondary structure, {beta}-contact and tertiary structure prediction of transmembrane {beta}-barrel proteins
Bioinformatics, February 15, 2008; 24(4): 513 - 520.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
K. Hinsen
Structural flexibility in proteins: impact of the crystal environment
Bioinformatics, February 15, 2008; 24(4): 521 - 528.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
D. Gront and A. Kolinski
Utility library for structural bioinformatics
Bioinformatics, February 15, 2008; 24(4): 584 - 585.
[Abstract] [Full Text] [PDF]


Home page
RNAHome page
A. Montanari, C. Besagni, C. De Luca, V. Morea, R. Oliva, A. Tramontano, M. Bolotin-Fukuhara, L. Frontali, and S. Francisci
Yeast as a model of human mitochondrial tRNA base substitutions: Investigation of the molecular basis of respiratory defects
RNA, February 1, 2008; 14(2): 275 - 283.
[Abstract] [Full Text] [PDF]


Home page
Protein Sci.Home page
W. J. Metzler, J. Yanchunas, C. Weigelt, K. Kish, H. E. Klei, D. Xie, Y. Zhang, M. Corbett, J. K. Tamura, B. He, et al.
Involvement of DPP-IV catalytic residues in enzyme-saxagliptin complex formation
Protein Sci., February 1, 2008; 17(2): 240 - 250.
[Abstract] [Full Text] [PDF]


Home page
Protein Eng Des SelHome page
T. Ikura, K. Kinoshita, and N. Ito
A cavity with an appropriate size is the basis of the PPIase activity
Protein Eng. Des. Sel., February 1, 2008; 21(2): 83 - 89.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
Q. Kaas, J.-C. Westermann, R. Halai, C. K. L. Wang, and D. J. Craik
ConoServer, a database for conopeptide sequences and structures
Bioinformatics, February 1, 2008; 24(3): 445 - 446.
[Abstract] [Full Text] [PDF]


Home page
Protein Sci.Home page
C. Papaloukas, E. Granseth, H. Viklund, and A. Elofsson
Estimating the length of transmembrane helices using Z-coordinate predictions
Protein Sci., February 1, 2008; 17(2): 271 - 278.
[Abstract] [Full Text] [PDF]


Home page
BioinformaticsHome page
M. J. Sippl and M. Wiederstein
A note on difficult structure alignment problems
Bioinformatics, February 1, 2008; 24(3): 426 - 427.
[Abstract] [Full Text] [PDF]


Home page
Biophys. JHome page
S. E. D. Webb, S. K. Roberts, S. R. Needham, C. J. Tynan, D. J. Rolfe, M. D. Winn, D. T. Clarke, R. Barraclough, and M. L. Martin-Fernandez
Single-Molecule Imaging and Fluorescence Lifetime Imaging Microscopy Show Different Structures for High- and Low-Affinity Epidermal Growth Factor Receptors in A431 Cells
Biophys. J., February 1, 2008; 94(3): 803 - 819.
[Abstract] [Full Text] [PDF]


Home page
Biophys. JHome page
H. Chen and J. Skolnick
M-TASSER: An Algorithm for Protein Quaternary Structure Prediction
Biophys. J., February 1, 2008; 94(3): 918 - 928.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
B. W. Shen, P. C. Spiegel, C.-H. Chang, J.-W. Huh, J.-S. Lee, J. Kim, Y.-H. Kim, and B. L. Stoddard
The tertiary structure and domain organization of coagulation factor VIII
Blood, February 1, 2008; 111(3): 1240 - 1247.
[Abstract] [Full Text] [PDF]


Home page
Biophys. JHome page
X. Han, K. Hristova, and W. C. Wimley
Protein Folding in Membranes: Insights from Neutron Diffraction Studies of a Membrane -Sheet Oligomer
Biophys. J., January 15, 2008; 94(2): 492 - 505.
[Abstract] [Full Text] [PDF]


Home page
BloodHome page
R. Ajjan, B. C. B. Lim, K. F. Standeven, R. Harrand, S. Dolling, F. Phoenix, R. Greaves, R. H. Abou-Saleh, S. Connell, D. A. M. Smith, et al.
Common variation in the C-terminal region of the fibrinogen -chain: effects on fibrin structure, fibrinolysis and clot rigidity
Blood, January 15, 2008; 111(2): 643 - 650.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
A. Pati, Y. Jin, K. Klage, R. F. Helm, L. S. Heath, and N. Ramakrishnan
CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D69 - D76.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
B. Raghavachari, A. Tasneem, T. M. Przytycka, and R. Jothi
DOMINE: a database of protein domain interactions
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D656 - D661.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
G. E. Tusnady, L. Kalmar, and I. Simon
TOPDB: topology data bank of transmembrane proteins
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D234 - D239.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
M. Popenda, M. Blazewicz, M. Szachniuk, and R. W. Adamiak
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D386 - D391.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
C. J. Reedy, M. M. Elvekrog, and B. R. Gibney
Development of a heme protein structure electrochemical function database
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D307 - D313.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
B. H. Dessailly, M. F. Lensink, C. A. Orengo, and S. J. Wodak
LigASite a database of biologically relevant binding sites in proteins with known apo-structures
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D667 - D673.
[Abstract] [Full Text] [PDF]


Home page
Nucleic Acids ResHome page
E. Bindewald, R. Hayes, Y. G. Yingling, W. Kasprzak, and B. A. Shapiro
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D392 - D397.
[Abstract] [Full Text] [PDF]