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

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.

Structure, March 7, 2017, Vol.25(3), p.536 [Periódico revisado por pares]

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  • Título:
    OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.(Report)
  • Autor: 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.
  • Assuntos: Information Management ; Molecular Biology ; Workflow Software
  • É parte de: Structure, March 7, 2017, Vol.25(3), p.536
  • Descrição: To access, purchase, authenticate, or subscribe to the full-text of this article, please visit this link: http://dx.doi.org/10.1016/j.str.2017.01.004 Byline: Jasmine Y. Young [jasmine.young@rcsb.org] (1,12,*), John D. Westbrook (1), Zukang Feng (1), Raul Sala (1), Ezra Peisach (1), Thomas J. Oldfield (2,9), Sanchayita Sen (2), Aleksandras Gutmanas (2), David R. Armstrong (2), John M. Berrisford (2), Li Chen (1), Minyu Chen (3), Luigi Di Costanzo (1), Dimitris Dimitropoulos (1,10), Guanghua Gao (1), Sutapa Ghosh (1), Swanand Gore (2), Vladimir Guranovic (1), Pieter M.S. Hendrickx (2), Brian P. Hudson (1), Reiko Igarashi (3), Yasuyo Ikegawa (3), Naohiro Kobayashi (3), Catherine L. Lawson (1), Yuhe Liang (1), Steve Mading (4), Lora Mak (2), M. Saqib Mir (2), Abhik Mukhopadhyay (2), Ardan Patwardhan (2), Irina Persikova (1), Luana Rinaldi (2), Eduardo Sanz-Garcia (2), Monica R. Sekharan (1), Chenghua Shao (1), G. Jawahar Swaminathan (2,11), Lihua Tan (1), Eldon L. Ulrich (4), Glen van Ginkel (2), Reiko Yamashita (3), Huanwang Yang (1), Marina A. Zhuravleva (1), Martha Quesada (1), Gerard J. Kleywegt (2), Helen M. Berman (1), John L. Markley (4), Haruki Nakamura (3), Sameer Velankar (2), Stephen K. Burley (1,5,6,7,8) Keywords Protein Data Bank; PDB; wwPDB; validation; data archiving; 3D macromolecular structure; structural biology; research data; data deposition; biocuration Highlights * wwPDB has deployed a unified wwPDB OneDep system globally * wwPDB has improved structure validation using community widely adopted software * The processing efficiency in biocuration is improved via more automated workflow Summary OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments. Author Affiliation: (1) RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (2) Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK (3) PDBj, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan (4) BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA (5) RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA (6) Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA (7) Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA (8) Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA * Corresponding author Article History: Received 30 September 2016; Revised 8 November 2016; Accepted 10 January 2017 (miscellaneous) Published: February 9, 2017 (footnote)9 Present address: Dotmatics, The Old Monastery, Windhill, Bishops Stortford, Herts CM23 2ND, UK (footnote)10 Present address: Google, Irvine, CA 92612, USA (footnote)11 Present address: Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford CB10 1XL, UK (footnote)12 Lead Contact
  • Idioma: Inglês

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