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Chemical annotation of small and peptide-like molecules at the Protein Data Bank

Descriptive

TypeOfResource
Text
TitleInfo
Title
Chemical annotation of small and peptide-like molecules at the Protein Data Bank
Name (type = personal)
NamePart (type = family)
Young
NamePart (type = given)
Jasmine Y.
Affiliation
Proteomics, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Feng
NamePart (type = given)
Zukang
Affiliation
Proteomics, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Dimitropoulos
NamePart (type = given)
Dimitris
Affiliation
San Diego Supercomputer Centre and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Sala
NamePart (type = given)
Raul
Affiliation
Proteomics, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Westbrook
NamePart (type = given)
John
Affiliation
Proteomics, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Zhuravleva
NamePart (type = given)
Marina
Affiliation
Proteomics, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Shao
NamePart (type = given)
Chenghua
Affiliation
Proteomics, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Quesada
NamePart (type = given)
Martha
Affiliation
Proteomics, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Peisach
NamePart (type = given)
Ezra
Affiliation
Proteomics, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = personal)
NamePart (type = family)
Berman
NamePart (type = given)
Helen M.
Affiliation
Chemistry & Chemical Biology, Rutgers University
Role
RoleTerm (type = text); (authority = marcrt)
author
Name (type = corporate); (authority = RutgersOrg-Department)
NamePart
Proteomics
Name (type = corporate); (authority = RutgersOrg-Department)
NamePart
Chemistry & Chemical Biology
Name (type = corporate); (authority = RutgersOrg-School)
NamePart
School of Arts and Sciences (SAS) (New Brunswick)
Genre (authority = RULIB-FS)
Article, Refereed
Genre (authority = NISO JAV)
Version of Record (VoR)
Note (type = peerReview)
Peer reviewed
OriginInfo
DateIssued (encoding = w3cdtf); (keyDate = yes)
2013
Abstract (type = Abstract)
Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality.
Language
LanguageTerm (authority = ISO 639-3:2007); (type = text)
English
PhysicalDescription
InternetMediaType
application/pdf
Extent
9 p.
Subject (authority = local)
Topic
Biocuration
Subject (authority = local)
Topic
Annotation
Subject (authority = local)
Topic
Macromolecular structure
Subject (authority = local)
Topic
Data archive
Subject (authority = local)
Topic
mmCIF data dictionary
Subject (authority = local)
Topic
Controlled vocabulary
Subject (authority = local)
Topic
Validation
Extension
DescriptiveEvent
Type
Citation
DateTime (encoding = w3cdtf)
2013
AssociatedObject
Name
Database
Type
Journal
Relationship
Has part
Detail
bat079
Identifier (type = volume and issue)
2013
Reference (type = url)
http://dx.doi.org/10.1093/database/bat079
Extension
DescriptiveEvent
Type
Grant award
AssociatedEntity
Role
Funder
Name
National Science Foundation
AssociatedEntity
Role
Originator
Name
Stephen K. Burley
AssociatedObject
Type
Grant number
Name
DBI-1338415
Subject
Name (authority = LCNAF)
NamePart (type = corporate)
Worldwide Protein Databank (wwPDB)
RelatedItem (type = host)
TitleInfo
Title
Young, Jasmine Y.
Identifier (type = local)
rucore30237700001
RelatedItem (type = host)
TitleInfo
Title
Feng, Zukang
Identifier (type = local)
rucore30238100001
RelatedItem (type = host)
TitleInfo
Title
Sala, Raul
Identifier (type = local)
rucore30238200001
RelatedItem (type = host)
TitleInfo
Title
Westbrook, John
Identifier (type = local)
rucore30238300001
RelatedItem (type = host)
TitleInfo
Title
Zhuravleva, Marina
Identifier (type = local)
rucore30238400001
RelatedItem (type = host)
TitleInfo
Title
Shao, Chenghua
Identifier (type = local)
rucore30238500001
RelatedItem (type = host)
TitleInfo
Title
Peisach, Ezra
Identifier (type = local)
rucore30238600001
RelatedItem (type = host)
TitleInfo
Title
Berman, Helen M.
Identifier (type = local)
rucore30238700001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/T300051M
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Rights

RightsDeclaration (AUTHORITY = FS); (ID = rulibRdec0004)
Copyright for scholarly resources published in RUcore is retained by the copyright holder. By virtue of its appearance in this open access medium, you are free to use this resource, with proper attribution, in educational and other non-commercial settings. Other uses, such as reproduction or republication, may require the permission of the copyright holder.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
RightsEvent
Type
Permission or license
AssociatedObject
Type
License
Name
Multiple author license v. 1
Detail
I hereby grant to Rutgers, The State University of New Jersey (Rutgers) the non-exclusive right to retain, reproduce, and distribute the deposited work (Work) in whole or in part, in and from its electronic format, without fee. This agreement does not represent a transfer of copyright to Rutgers.Rutgers may make and keep more than one copy of the Work for purposes of security, backup, preservation, and access and may migrate the Work to any medium or format for the purpose of preservation and access in the future. Rutgers will not make any alteration, other than as allowed by this agreement, to the Work.I represent and warrant to Rutgers that the Work is my original work. I also represent that the Work does not, to the best of my knowledge, infringe or violate any rights of others.I further represent and warrant that I have obtained all necessary rights to permit Rutgers to reproduce and distribute the Work and that any third-party owned content is clearly identified and acknowledged within the Work.By granting this license, I acknowledge that I have read and agreed to the terms of this agreement and all related RUcore and Rutgers policies.
RightsEvent
Type
Embargo
DateTime (encoding = w3cdtf); (point = end); (qualifier = exact); (keyDate = no)
2173-10-02
DateTime (encoding = w3cdtf); (point = start); (qualifier = exact); (keyDate = no)
2017-10-02
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after: 2173-10-02
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Technical

RULTechMD (ID = TECHNICAL1)
ContentModel
Document
CreatingApplication
Version
1.3
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2013-11-27T11:43:26
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2013-11-27T11:43:26
ApplicationName
Adobe LiveCycle PDFG ES
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