Validation of Structures in the Protein Data Bank

Gore, Swanand; Sanz García, Eduardo; Hendrickx, Pieter M. S.; Gutmanas, Aleksandras; Westbrook, John D.; Yang, Huanwang; Feng, Zukang; Baskaran, Kumaran; Berrisford, John M.; Hudson, Brian P.; Ikegawa, Yasuyo; Kobayashi, Naohiro; Lawson, Catherine L.; Mading, Steve; Mak, Lora; Mukhopadhyay, Abhik; Oldfield, Thomas J.; Patwardhan, Ardan; Peisach, Ezra; Sahni, Gaurav; Sekharan, Monica R.; Sen, Sanchayita; Shao, Chenghua; Smart, Oliver S.; Ulrich, Eldon L.; Yamashita, Reiko; Quesada, Martha; Young, Jasmine Y.; Nakamura, Haruki; Markley, John L.; Berman, Helen M.; Burley, Stephen K.; Velankar, Sameer; Kleywegt, Gerard J.

doi:10.1016/j.str.2017.10.009

Title: Validation of Structures in the Protein Data Bank

Journal Article · 01 December 2017 · Structure

DOI: https://doi.org/10.1016/j.str.2017.10.009 · OSTI ID:1410138

Gore, Swanand ^[1]; Sanz García, Eduardo ^[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. ^[4]; Hudson, Brian P. ^[2]; Ikegawa, Yasuyo ^[5]; Kobayashi, Naohiro ^[5]; Lawson, Catherine L. ^[2]; Mading, Steve ^[3]; Mak, Lora ^[4]; Mukhopadhyay, Abhik ^[4]; Oldfield, Thomas J. ^[4]; Patwardhan, Ardan ^[4]; Peisach, Ezra ^[2]; Sahni, Gaurav ^[4] more »

European Molecular Biology Lab. (EMBL), Cambridge (United Kingdom). European Bioinformatics Inst. (ELBL-EBI). Protein Data Bank in Europe (PDBe). Wellcome Genome Campus
Rutgers Univ., Piscataway, NJ (United States). Center for Integrative Proteomics Research. RCSB Protein Data Bank
Univ. of Wisconsin, Madison, WI (United States). BioMagResBank (BMRB)
European Molecular Biology Lab. (EMBL), Cambridge (United Kingdom). European Bioinformatics Inst. (ELBL-EBI). Protein Data Bank in Europe (PDBe). Wellcome Genome Campus
Osaka Univ. (Japan). Inst. for Protein Research. PDBj
Rutgers Univ., Piscataway, NJ (United States). Center for Integrative Proteomics Research. RCSB Protein Data Bank; Univ. of California, La Jolla, CA (United States). Sand Diego Supercomputer Center. RCSB Protein Data Bank; Univ. of California, La Jolla, CA (United States). Skaggs School of Pharmacy and Pharmaceutical Sciences; Rutgers Univ., Piscataway, NJ (United States). Inst. for Quantitative Biomedicine

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.

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Research Organization:: Rutgers Univ., Piscataway, NJ (United States)

Sponsoring Organization:: USDOE Office of Science (SC); USDOE

Grant/Contract Number:: FG02-00ER41132; DBI-1338415

OSTI ID:: 1410138

Alternate ID(s):: OSTI ID: 1623723

Journal Information:: Structure, Vol. 25, Issue 12; ISSN 0969-2126

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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