Validation of Structures in the Protein Data Bank
Abstract
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.
- Authors:
- more »
- Publication Date:
- Research Org.:
- Rutgers Univ., Piscataway, NJ (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1410138
- Alternate Identifier(s):
- OSTI ID: 1623723
- Grant/Contract Number:
- DBI-1338415; FG02-00ER41132
- Resource Type:
- Published Article
- Journal Name:
- Structure
- Additional Journal Information:
- Journal Name: Structure Journal Volume: 25 Journal Issue: 12; Journal ID: ISSN 0969-2126
- Publisher:
- Elsevier
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Biophysics; Cell Biology
Citation Formats
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, and Kleywegt, Gerard J.. Validation of Structures in the Protein Data Bank. United Kingdom: N. p., 2017.
Web. doi:10.1016/j.str.2017.10.009.
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.. Validation of Structures in the Protein Data Bank. United Kingdom. https://doi.org/10.1016/j.str.2017.10.009
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, and Kleywegt, Gerard J.. Fri .
"Validation of Structures in the Protein Data Bank". United Kingdom. https://doi.org/10.1016/j.str.2017.10.009.
@article{osti_1410138,
title = {Validation of Structures in the Protein Data Bank},
author = {Gore, Swanand and Sanz García, Eduardo and Hendrickx, Pieter M. S. and Gutmanas, Aleksandras and Westbrook, John D. and Yang, Huanwang and Feng, Zukang and Baskaran, Kumaran and Berrisford, John M. and Hudson, Brian P. and Ikegawa, Yasuyo and Kobayashi, Naohiro and Lawson, Catherine L. and Mading, Steve and Mak, Lora and Mukhopadhyay, Abhik and Oldfield, Thomas J. and Patwardhan, Ardan and Peisach, Ezra and Sahni, Gaurav and Sekharan, Monica R. and Sen, Sanchayita and Shao, Chenghua and Smart, Oliver S. and Ulrich, Eldon L. and Yamashita, Reiko and Quesada, Martha and Young, Jasmine Y. and Nakamura, Haruki and Markley, John L. and Berman, Helen M. and Burley, Stephen K. and Velankar, Sameer and Kleywegt, Gerard J.},
abstractNote = {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.},
doi = {10.1016/j.str.2017.10.009},
journal = {Structure},
number = 12,
volume = 25,
place = {United Kingdom},
year = {2017},
month = {12}
}
https://doi.org/10.1016/j.str.2017.10.009
Web of Science
Figures / Tables:

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Figures / Tables found in this record: