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Title: Validation of Structures in the Protein Data Bank

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »; ; ; ; ; ; ; ; ; ; ; ; ; ; « less
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1410138
Grant/Contract Number:
DBI-1338415
Resource Type:
Journal Article: Published Article
Journal Name:
Structure
Additional Journal Information:
Related Information: CHORUS Timestamp: 2017-11-23 06:01:47; Journal ID: ISSN 0969-2126
Publisher:
Elsevier
Country of Publication:
United Kingdom
Language:
English

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. 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, and Kleywegt, Gerard J. 2017. "Validation of Structures in the Protein Data Bank". United Kingdom. doi: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 = {},
doi = {10.1016/j.str.2017.10.009},
journal = {Structure},
number = ,
volume = ,
place = {United Kingdom},
year = 2017,
month =
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1016/j.str.2017.10.009

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  • The implementation of a validation pipeline, based on community recommendations, for future depositions of X-ray crystal structures in the Protein Data Bank is described. There is an increasing realisation that the quality of the biomacromolecular structures deposited in the Protein Data Bank (PDB) archive needs to be assessed critically using established and powerful validation methods. The Worldwide Protein Data Bank (wwPDB) organization has convened several Validation Task Forces (VTFs) to advise on the methods and standards that should be used to validate all of the entries already in the PDB as well as all structures that will be deposited inmore » the future. The recommendations of the X-ray VTF are currently being implemented in a software pipeline. Here, ongoing work on this pipeline is briefly described as well as ways in which validation-related information could be presented to users of structural data.« less
  • Here, protein-protein interactions are ubiquitous and essential for cellular processes. High-resolution X-ray crystallographic structures of protein complexes can elucidate the details of their function and provide a basis for many computational and experimental approaches. Here we demonstrate that existing annotations of protein complexes, including those provided by the Protein Data Bank (PDB) itself, contain a significant fraction of incorrect annotations. Results: We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster ismore » relevant based on a diverse set of properties; and (4) finally combining these scores for each entry in order to predict the complex structure. Unlike previous annotation methods, consistent prediction of complexes with identical or almost identical protein content is insured. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions.« less
  • The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) resource provides tools for query, analysis and visualization of the 3D structures in the PDB archive. As the mobile Web is starting to surpass desktop and laptop usage, scientists and educators are beginning to integrate mobile devices into their research and teaching. In response, we have developed the RCSB PDB Mobile app for the iOS and Android mobile platforms to enable fast and convenient access to RCSB PDB data and services. Lastly, using the app, users from the general public to expert researchers can quickly search and visualize biomolecules,more » and add personal annotations via the RCSB PDB's integrated MyPDB service.« less
  • The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). Here, an analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.