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Literature DB >> 10592235

The Protein Data Bank.

H M Berman¹, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne.

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.

Mesh：

Substances：
Proteins

Year: 2000 PMID： 10592235 PMCID： PMC102472 DOI： 10.1093/nar/28.1.235

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

24 in total

1. GRASS: a server for the graphical representation and analysis of structures.

Authors: M Nayal; B C Hitz; B Honig
Journal: Protein Sci Date: 1999-03 Impact factor: 6.725

2. Macromolecular structure databases: past progress and future challenges.

Authors: H Weissig; I N Shindyalov; P E Bourne
Journal: Acta Crystallogr D Biol Crystallogr Date: 1998-11-01

3. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

Authors: A A Vaguine; J Richelle; S J Wodak
Journal: Acta Crystallogr D Biol Crystallogr Date: 1999-01-01

4. Macromolecular Crystallographic Information File.

Authors: P E Bourne; H M Berman; B McMahon; K D Watenpaugh; J D Westbrook; P M Fitzgerald
Journal: Methods Enzymol Date: 1997 Impact factor: 1.600

5. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.

Authors: I N Shindyalov; P E Bourne
Journal: Protein Eng Date: 1998-09

6. 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.

Authors: J L Markley; A Bax; Y Arata; C W Hilbers; R Kaptein; B D Sykes; P E Wright; K Wüthrich
Journal: J Biomol NMR Date: 1998-07 Impact factor: 2.835

The Protein Data Bank.

1. GRASS: a server for the graphical representation and analysis of structures.

2. Macromolecular structure databases: past progress and future challenges.

3. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

4. Macromolecular Crystallographic Information File.

5. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.

6. 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.

Review 7. Surprising similarities in structure comparison.

8. Improved tools for biological sequence comparison.

9. Creation of a nuclear magnetic resonance data repository and literature database.

10. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

1. MMDB: 3D structure data in Entrez.

2. Exploring steric constraints on protein mutations using MAGE/PROBE.

3. Polar side chains drive the association of model transmembrane peptides.

4. The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes.

5. The PDB data uniformity project.

6. CKAAPs DB: a conserved key amino acid positions database.

7. PDBsum: summaries and analyses of PDB structures.

8. A rapid classification protocol for the CATH Domain Database to support structural genomics.

9. Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.

10. The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.