Validation of Structures in the Protein Data Bank

被引：175

作者：

Gore, Swanand ^{[1
]}

Garcia, Eduardo Sanz ^{[1
]}

Hendrickx, Pieter M. S. ^{[1
]}

Gutmanas, Aleksandras ^{[1
]}

Westbrook, John D. ^{[2
]}

Yang, Huanwang ^{[2
]}

Feng, Zukang ^{[2
]}

Baskaran, Kumaran ^{[3
]}

Berrisford, John M. ^{[1
]}

Hudson, Brian P. ^{[2
]}

Ikegawa, Yasuyo ^{[4
]}

Kobayashi, Naohiro ^{[4
]}

Lawson, Catherine L. ^{[2
]}

Mading, Steve ^{[3
]}

Mak, Lora ^{[1
]}

Mukhopadhyay, Abhik ^{[1
]}

Oldfield, Thomas J. ^{[1
,9
]}

Patwardhan, Ardan ^{[1
]}

Peisach, Ezra ^{[2
]}

Sahni, Gaurav ^{[1
]}

Sekharan, Monica R. ^{[2
]}

Sen, Sanchayita ^{[1
]}

Shao, Chenghua ^{[2
]}

Smart, Oliver S. ^{[1
]}

Ulrich, Eldon L. ^{[3
]}

Yamashita, Reiko ^{[4
]}

Quesada, Martha ^{[2
]}

Young, Jasmine Y. ^{[2
]}

Nakamura, Haruki ^{[4
]}

Markley, John L. ^{[3
]}

Berman, Helen M. ^{[2
]}

Burley, Stephen K. ^{[2
,5
,6
,7
,8
]}

Velankar, Sameer ^{[1
]}

Kleywegt, Gerard J. ^{[1
]}

机构：

[1] EBI, EMBL, PDBe, Wellcome Genome Campus, Cambridge CB10 1SD, England

[2] Rutgers State Univ, RCSB Prot Data Bank, Ctr Integrat Prote Res, Piscataway, NJ 08854 USA

[3] Univ Wisconsin, BMRB, BioMagResBank, Madison, WI 53706 USA

[4] Osaka Univ, Inst Prot Res, PDBj, Suita, Osaka 5650871, Japan

[5] Univ Calif San Diego, RCSB Prot Data Bank, San Diego Supercomp Ctr, La Jolla, CA 92093 USA

[6] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92093 USA

[7] Rutgers State Univ, Inst Quantitat Biomed, Piscataway, NJ 08854 USA

[8] Rutgers State Univ, Rutgers Canc Inst New Jersey, New Brunswick, NJ 08903 USA

[9] Dotmatics, Windhill, Bishops Stortford CM23 2ND, Herts, England

来源：

STRUCTURE | 2017年 / 25卷 / 12期

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会; 美国国家科学基金会;

关键词：

MACROMOLECULAR STRUCTURES; PDB; REFINEMENT; RESOURCE; SYSTEM; TOOLS;

D O I：

10.1016/j.str.2017.10.009

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.

引用

页码：1916 / 1927

页数：12

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