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Protein Data Bank

About: Protein Data Bank is a(n) research topic. Over the lifetime, 2265 publication(s) have been published within this topic receiving 174153 citation(s). The topic is also known as: PDB.
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Journal ArticleDOI
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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.

30,190 citations


Journal ArticleDOI
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.
Abstract: The Protein Data Bank is a computer-based archival file for macromolecular structures The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies Text included in each data entry gives pertinent information for the structure at hand (eg species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure) In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americans), Tokyo (Japan), and Cambridge (Europe and worldwide) A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (eg α-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures

7,901 citations


Journal ArticleDOI
TL;DR: A new method, based on chemical thermodynamics, is developed for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments, as found, biological units may be recovered at 80-90% success rate, which makesX-ray crystallography an important source of experimental data on macromolescular complexes and protein-protein interactions.
Abstract: We discuss basic physical-chemical principles underlying the formation of stable macromolecular complexes, which in many cases are likely to be the biological units performing a certain physiological function We also consider available theoretical approaches to the calculation of macromolecular affinity and entropy of complexation The latter is shown to play an important role and make a major effect on complex size and symmetry We develop a new method, based on chemical thermodynamics, for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments As found, biological units may be recovered at 80-90% success rate, which makes X-ray crystallography an important source of experimental data on macromolecular complexes and protein-protein interactions The method is implemented as a public WWW service

7,202 citations


Journal ArticleDOI
TL;DR: The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities.
Abstract: The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input. The output is a colour, or black-and-white, PostScript file giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities. The program is completely general for any ligand and can also be used to show other types of interaction in proteins and nucleic acids. It was designed to facilitate the rapid inspection of many enzyme complexes, but has found many other applications.

4,180 citations


Journal ArticleDOI
TL;DR: The key purpose of interactive analysis is to check whether conserved residues line up in multiple structural alignments and how Conserved residues and ligands cluster together in multiple structure superimpositions.
Abstract: Our web site (http://ekhidna.biocenter.helsinki.fi/dali_server) runs the Dali program for protein structure comparison. The web site consists of three parts: (i) the Dali server compares newly solved structures against structures in the Protein Data Bank (PDB), (ii) the Dali database allows browsing precomputed structural neighbourhoods and (iii) the pairwise comparison generates suboptimal alignments for a pair of structures. Each part has its own query form and a common format for the results page. The inputs are either PDB identifiers or novel structures uploaded by the user. The results pages are hyperlinked to aid interactive analysis. The web interface is simple and easy to use. The key purpose of interactive analysis is to check whether conserved residues line up in multiple structural alignments and how conserved residues and ligands cluster together in multiple structure superimpositions. In favourable cases, protein structure comparison can lead to evolutionary discoveries not detected by sequence analysis.

3,347 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2021135
2020130
2019112
201894
2017117
201695

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Topic's top 5 most impactful authors

Helen M. Berman

70 papers, 39.9K citations

John D. Westbrook

48 papers, 38.1K citations

Stephen K. Burley

40 papers, 2.5K citations

Philip E. Bourne

29 papers, 35.2K citations

Zukang Feng

20 papers, 34.9K citations