OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Young, Jasmine Y.; Westbrook, John D.; Feng, Zukang; Sala, Raul; Peisach, Ezra; Oldfield, Thomas J.; Sen, Sanchayita; Gutmanas, Aleksandras; Armstrong, David R.; Berrisford, John M.; Chen, Li; Chen, Minyu; Di Costanzo, Luigi; Dimitropoulos, Dimitris; Gao, Guanghua; Ghosh, Sutapa; Gore, Swanand; Guranovic, Vladimir; Hendrickx, Pieter M. S.; Hudson, Brian P.; Igarashi, Reiko; Ikegawa, Yasuyo; Kobayashi, Naohiro; Lawson, Catherine L.; Liang, Yuhe; Mading, Steve; Mak, Lora; Mir, M. Saqib; Mukhopadhyay, Abhik; Patwardhan, Ardan; Persikova, Irina; Rinaldi, Luana; Sanz-Garcia, Eduardo; Sekharan, Monica R.; Shao, Chenghua; Swaminathan, G. Jawahar; Tan, Lihua; Ulrich, Eldon L.; van Ginkel, Glen; Yamashita, Reiko; Yang, Huanwang; Zhuravleva, Marina A.; Quesada, Martha; Kleywegt, Gerard J.; Berman, Helen M.; Markley, John L.; Nakamura, Haruki; Velankar, Sameer; Burley, Stephen K.

doi:10.1016/j.str.2017.01.004

Title: OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

Full Record
Other Related Research

Authors:: Young, Jasmine Y.; Westbrook, John D.; Feng, Zukang; Sala, Raul; Peisach, Ezra; Oldfield, Thomas J.; Sen, Sanchayita; Gutmanas, Aleksandras; Armstrong, David R.; Berrisford, John M.; Chen, Li; Chen, Minyu; Di Costanzo, Luigi; Dimitropoulos, Dimitris; Gao, Guanghua; Ghosh, Sutapa; Gore, Swanand; Guranovic, Vladimir; Hendrickx, Pieter M. S.; Hudson, Brian P. more »« less

Publication Date:: 2017-03-01

Sponsoring Org.:: USDOE

OSTI Identifier:: 1424512

Alternate Identifier(s):: OSTI ID: 1410135

Resource Type:: Published Article

Journal Name:: Structure

Additional Journal Information:: Journal Name: Structure Journal Volume: 25 Journal Issue: 3; Journal ID: ISSN 0969-2126

Publisher:: Elsevier

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Young, Jasmine Y., Westbrook, John D., Feng, Zukang, Sala, Raul, Peisach, Ezra, Oldfield, Thomas J., Sen, Sanchayita, Gutmanas, Aleksandras, Armstrong, David R., Berrisford, John M., Chen, Li, Chen, Minyu, Di Costanzo, Luigi, Dimitropoulos, Dimitris, Gao, Guanghua, Ghosh, Sutapa, Gore, Swanand, Guranovic, Vladimir, Hendrickx, Pieter M. S., Hudson, Brian P., Igarashi, Reiko, Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Liang, Yuhe, Mading, Steve, Mak, Lora, Mir, M. Saqib, Mukhopadhyay, Abhik, Patwardhan, Ardan, Persikova, Irina, Rinaldi, Luana, Sanz-Garcia, Eduardo, Sekharan, Monica R., Shao, Chenghua, Swaminathan, G. Jawahar, Tan, Lihua, Ulrich, Eldon L., van Ginkel, Glen, Yamashita, Reiko, Yang, Huanwang, Zhuravleva, Marina A., Quesada, Martha, Kleywegt, Gerard J., Berman, Helen M., Markley, John L., Nakamura, Haruki, Velankar, Sameer, and Burley, Stephen K. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.  United Kingdom: N. p., 2017. 
Web.  doi:10.1016/j.str.2017.01.004.

Copy to clipboard


                    Young, Jasmine Y., Westbrook, John D., Feng, Zukang, Sala, Raul, Peisach, Ezra, Oldfield, Thomas J., Sen, Sanchayita, Gutmanas, Aleksandras, Armstrong, David R., Berrisford, John M., Chen, Li, Chen, Minyu, Di Costanzo, Luigi, Dimitropoulos, Dimitris, Gao, Guanghua, Ghosh, Sutapa, Gore, Swanand, Guranovic, Vladimir, Hendrickx, Pieter M. S., Hudson, Brian P., Igarashi, Reiko, Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Liang, Yuhe, Mading, Steve, Mak, Lora, Mir, M. Saqib, Mukhopadhyay, Abhik, Patwardhan, Ardan, Persikova, Irina, Rinaldi, Luana, Sanz-Garcia, Eduardo, Sekharan, Monica R., Shao, Chenghua, Swaminathan, G. Jawahar, Tan, Lihua, Ulrich, Eldon L., van Ginkel, Glen, Yamashita, Reiko, Yang, Huanwang, Zhuravleva, Marina A., Quesada, Martha, Kleywegt, Gerard J., Berman, Helen M., Markley, John L., Nakamura, Haruki, Velankar, Sameer, & Burley, Stephen K. OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.  United Kingdom.  https://doi.org/10.1016/j.str.2017.01.004

Copy to clipboard


                    Young, Jasmine Y., Westbrook, John D., Feng, Zukang, Sala, Raul, Peisach, Ezra, Oldfield, Thomas J., Sen, Sanchayita, Gutmanas, Aleksandras, Armstrong, David R., Berrisford, John M., Chen, Li, Chen, Minyu, Di Costanzo, Luigi, Dimitropoulos, Dimitris, Gao, Guanghua, Ghosh, Sutapa, Gore, Swanand, Guranovic, Vladimir, Hendrickx, Pieter M. S., Hudson, Brian P., Igarashi, Reiko, Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Liang, Yuhe, Mading, Steve, Mak, Lora, Mir, M. Saqib, Mukhopadhyay, Abhik, Patwardhan, Ardan, Persikova, Irina, Rinaldi, Luana, Sanz-Garcia, Eduardo, Sekharan, Monica R., Shao, Chenghua, Swaminathan, G. Jawahar, Tan, Lihua, Ulrich, Eldon L., van Ginkel, Glen, Yamashita, Reiko, Yang, Huanwang, Zhuravleva, Marina A., Quesada, Martha, Kleywegt, Gerard J., Berman, Helen M., Markley, John L., Nakamura, Haruki, Velankar, Sameer, and Burley, Stephen K. Wed .  
"OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive".  United Kingdom.  https://doi.org/10.1016/j.str.2017.01.004.

Copy to clipboard


                    
@article{osti_1424512,

  title        = {OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive},

  author       = {Young, Jasmine Y. and Westbrook, John D. and Feng, Zukang and Sala, Raul and Peisach, Ezra and Oldfield, Thomas J. and Sen, Sanchayita and Gutmanas, Aleksandras and Armstrong, David R. and Berrisford, John M. and Chen, Li and Chen, Minyu and Di Costanzo, Luigi and Dimitropoulos, Dimitris and Gao, Guanghua and Ghosh, Sutapa and Gore, Swanand and Guranovic, Vladimir and Hendrickx, Pieter M. S. and Hudson, Brian P. and Igarashi, Reiko and Ikegawa, Yasuyo and Kobayashi, Naohiro and Lawson, Catherine L. and Liang, Yuhe and Mading, Steve and Mak, Lora and Mir, M. Saqib and Mukhopadhyay, Abhik and Patwardhan, Ardan and Persikova, Irina and Rinaldi, Luana and Sanz-Garcia, Eduardo and Sekharan, Monica R. and Shao, Chenghua and Swaminathan, G. Jawahar and Tan, Lihua and Ulrich, Eldon L. and van Ginkel, Glen and Yamashita, Reiko and Yang, Huanwang and Zhuravleva, Marina A. and Quesada, Martha and Kleywegt, Gerard J. and Berman, Helen M. and Markley, John L. and Nakamura, Haruki and Velankar, Sameer and Burley, Stephen K.},

  abstractNote = {},

  doi          = {10.1016/j.str.2017.01.004},

  journal      = {Structure},

  number       = 3,

  volume       = 25,

  place        = {United Kingdom},

  year         = {2017},

  month        = {3}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Publisher's Version of Record
https://doi.org/10.1016/j.str.2017.01.004

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 24 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Similar Records in DOE PAGES and OSTI.GOV collections:

The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

Journal Article Berman, H. ; Henrick, K. ; Nakamura, H. ; ... - Nucleic Acids Research

The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission ofmore »« less
https://doi.org/10.1093/nar/gkl971

Full Text Available
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Journal Article Rose, Yana ; Duarte, Jose M. ; Lowe, Robert ; ... - Journal of Molecular Biology

The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves many millions of unique users worldwide by delivering experimentally-determined 3D structures of biomolecules integrated with >40 external data resources via RCSB.org, application programming interfaces (APIs), and FTP downloads. Herein, we present the architectural redesign of RCSB PDB data delivery services that build on existing PDBx/mmCIF data schemas. New data access APIs (data.rcsb.org) enable efficient delivery of all PDB archive data. A novel GraphQL-based API provides flexible, declarative data retrieval along with a simple-to-use REST API. A powerful new search system (search.rcsb.org) seamlessly integrates heterogeneous types of searchesmore »« less
https://doi.org/10.1016/j.jmb.2020.11.003
Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

Journal Article Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov ; Bricogne, Gerard ; Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 - Acta Crystallographica. Section D: Biological Crystallography

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray datamore »« less
https://doi.org/10.1107/S1399004714017040
Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

Journal Article Terwilliger, Thomas C. ; Bricogne, Gerard - Acta Crystallographica. Section D: Biological Crystallography (Online)

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when itmore »« less
Cited by 18
https://doi.org/10.1107/S1399004714017040

Full Text Available
Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive

Journal Article Shao, Chenghua ; Yang, Huanwang ; Westbrook, John D. ; ... - Structure
Cited by 7
https://doi.org/10.1016/j.str.2017.01.013

Similar Records