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PDBeCIF: an open-source mmCIF/CIF parsing and processing package

Glen van Ginkel, Lukáš Pravda, José M. Dana, Mihaly Varadi, Peter Keller, Stephen Anyango, Sameer Velankar
2021 BMC Bioinformatics  
The anticipated extension of the PDB small molecule identifiers defined by the Chemical Component Dictionary van Ginkel et al.  ...  The example shows code snippets and the result as a Python dictionary corresponding to an updated PDB entry "1cbs" section.van Ginkel et al. BMC Bioinformatics (2021) 22:383  ... 
doi:10.1186/s12859-021-04271-9 pmid:34301175 pmcid:PMC8299628 fatcat:vsufapo3bzeppeyvadnvn2z4ey

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

Sameer Velankar, José M. Dana, Julius Jacobsen, Glen van Ginkel, Paul J. Gane, Jie Luo, Thomas J. Oldfield, Claire O'Donovan, Maria-Jesus Martin, Gerard J. Kleywegt
2012 Nucleic Acids Research  
The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/ sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS
more » ... se. The SIFTS process includes crossreferences to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information.
doi:10.1093/nar/gks1258 pmid:23203869 pmcid:PMC3531078 fatcat:rnyow6huf5grfp5fz4oyien7zm

Straightforward and complete deposition of NMR data to the PDBe

Christopher J. Penkett, Glen van Ginkel, Sameer Velankar, Jawahar Swaminathan, Eldon L. Ulrich, Steve Mading, Tim J. Stevens, Rasmus H. Fogh, Aleksandras Gutmanas, Gerard J. Kleywegt, Kim Henrick, Wim F. Vranken
2010 Journal of Biomolecular NMR  
We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr
more » ... ter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at
doi:10.1007/s10858-010-9439-3 pmid:20680401 pmcid:PMC2950272 fatcat:dwh4dfnbavfvdgsnvgp3pemj34

PDBe: Protein Data Bank in Europe

Aleksandras Gutmanas, Younes Alhroub, Gary M. Battle, John M. Berrisford, Estelle Bochet, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Swanand P. Gore, Pauline Haslam, Rowan Hatherley (+15 others)
2013 Nucleic Acids Research  
The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such is actively engaged in the deposition, annotation, remediation and dissemination of macromolecular structure data through the single global archive for such data, the PDB. Similarly, PDBe is a member of the EMDataBank organisation (emdatabank.org), which manages the EMDB archive for electron microscopy data. PDBe also develops tools that help the biomedical science
more » ... nity to make effective use of the data in the PDB and EMDB for their research. Here we describe new or improved services, including updated SIFTS mappings to other bioinformatics resources, a new browser for the PDB archive based on Gene Ontology (GO) annotation, updates to the analysis of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.
doi:10.1093/nar/gkt1180 pmid:24288376 pmcid:PMC3965016 fatcat:rv2cpebl5ffzbdppo654oahfly

PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

Sameer Velankar, Glen van Ginkel, Younes Alhroub, Gary M. Battle, John M. Berrisford, Matthew J. Conroy, Jose M. Dana, Swanand P. Gore, Aleksandras Gutmanas, Pauline Haslam, Pieter M. S. Hendrickx, Ingvar Lagerstedt (+21 others)
2015 Nucleic Acids Research  
The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite
more » ... or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and upto-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and sup-port expert users in analysing macromolecular structure data.
doi:10.1093/nar/gkv1047 pmid:26476444 pmcid:PMC4702783 fatcat:sqjtb2p3drbjncdycqrfr3m2lm

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

Jasmine Y. Young, John D. Westbrook, Zukang Feng, Raul Sala, Ezra Peisach, Thomas J. Oldfield, Sanchayita Sen, Aleksandras Gutmanas, David R. Armstrong, John M. Berrisford, Li Chen, Minyu Chen (+37 others)
2017 Structure  
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
more » ... tion 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.
doi:10.1016/j.str.2017.01.004 pmid:28190782 pmcid:PMC5360273 fatcat:okamctypwvdrxfomgjio4rsvma

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Citation details: Young,J.Y., Westbrook,J.D., Feng,Z. et al. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The V C The Author(s) worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability,
more » ... ccessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a highquality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce

Page 432 of Current Geographical Publications Vol. 24, Issue 10 [page]

1961 Current Geographical Publications  
., 158 Gini, Corrado, 292 Ginkel, B. L. van, 113 Ginsburg, Norton, *145 Ginzburg, I. V., 263 Giorgi, Maurizio, 286 Girondin, France, 308 Giroux, P, R., 44 Girs, A. A., 107 Gittinger, J.  ...  V., 4 Glassburner, Bruce, 278 Gleason Creek, Nev., 46 Glen Canyon, Ariz., 200 Glen Canyon Dam, Ariz., 116, 302 Glen Coe, Scotland, 160 Glenn, C.  ... 

Remembering Jeanette Snyder Brown (1925–2014)

Winslow R. Briggs, Govindjee
2015 Photosynthesis Research  
Acknowledgments We are grateful to Jan Anderson and Gijs van Ginkel for their contribution to this paper.  ...  Gijs van Ginkel, of The Netherlands, wrote ''It is about 40 years ago that I first met Jan Brown.  ...  This led to a report in the Carnegie Yearbook and two papers van Ginkel 1979) ; this research was continued on a different track: the phase behavior of photosynthetic membranes and model membranes, consisting  ... 
doi:10.1007/s11120-015-0181-2 pmid:26314735 fatcat:gkbbtmh4d5h3xdnqcdhex2ojlq

Page 61 of Bibliography of Agriculture Vol. 30, Issue Index [page]

1966 Bibliography of Agriculture  
C H GIMMLER W GINDEL I GINOI I M EL GINDICH A GINER A GINGELL D J GINGRAS G GINGRICH JR GINGRICH S F GINIEIS C GINKEL J G VAN GINN H E GINOCCHIO S GINSBERG GINSBERG A 19315 A GINSBERG L M L E GINSBERG  ...  GILS J H J VAN GILST W J VAN GILT S GILYADOV ™ G GILYAROV MS 39270 GILYATZETDINOV S YA GIMBO A 20167 GIMENEZ ME GIMENEZ-MARTIN G 83221 83811 GIMENEZ-ORTIZ R GIMENO E J GIMESI A 9046 14597 35821 GIMINGHAM  ... 

Page 4570 of Bibliography of Agriculture. Annual Cumulative Indexes Vol. 60, Issue CUMULATIVE INDEX [page]

Bibliography of Agriculture. Annual Cumulative Indexes  
B. 1318400 Gingas, V.M. 1292609 Gingerich, W.H. 1299641 Ginkel, C.G. van 1277892 Ginkel, J.H. van. 1284949 Ginkel, M. van. 1285602 Ginkel, M. van 1309675 Ginn, M.L. 1284730 Ginn, P.E. 1271062, 1300098  ...  , D.M. 1274581, 1297664 Glen, J.W. 1281523 Glen, Samantha. 1314080 Glender, Eugene. 1278577 Glendinning, J.1. 1254908 Glendinning, PJ. 1314624 Glenn, B.P. 1272144 Glenn, D. 1262569 Glenn, D.M. 1267424,  ... 

Page 492 of National Union Catalog Vol. 55, Issue [page]

National Union Catalog  
Ginkel Jinkel, Henri Fievez de Malines van "ce Fievez ce valines van Ginkel, Ginlein, Rikhard Bduardovich see Gienlein Riknard Eduardovich 17-10 library of Congress Ginn, Edwin, 1838-1914 The international  ...  Sesten, Glen endless pany, 1686. Bp. 11, 0122, 157 — 19™. gy ey 1900. 2 English language—Study and teaching. 1. Goaay Idea jownt author 6 -30678 Liprary of Congress Leismce yaSe1; Gina, Fred B.  ... 

Page 4162 of Bibliography of Agriculture. Annual Cumulative Indexes Vol. 59, Issue Cumulative Index [page]

Bibliography of Agriculture. Annual Cumulative Indexes  
\u Oregon Coopera- tive Extension Service. 1206430 Ginkel, G. van. 1236352, 1236353, 1236355 Ginkcl, J.H. van. 1202039 Ginkel, M. van \u International Maize and Wheat Improvement Center, Mexico, Mexico  ...  \u CNRS, Gif sur Yvette, France. 1198737 Glen, D.M. 1194963, 1201339, 1224608 Glen, D. M. 1246613 Glen, D.M. 1248194 Glen, D.M.  ... 

Acknowledgement to Reviewers of Molecules in 2016

2017 Molecules  
Van Calenbergh, Serge van den Broek, Lambertus Van Den Ende, Wim Van Der Stelt, Mario Van Dyke, Knox Van Ginkel, Paul Van Griensven, Leo J. L.  ...  D Van Lanen, Steven Van Tassel, Paul Van Waardenburg, Robert C. A. M. Vanamala, Jairam K. P.  ... 
doi:10.3390/molecules22010113 fatcat:ixy6k72a5vfopnyt3xqbj2crfm

Page 1110 of Journal of Environmental Quality Vol. 30, Issue 3 [page]

Journal of Environmental Quality  
Dongen, S., University of Antwerp, Wilrijk, Belgium van Ginkel, C.G., AKZO Nobel Central Research, Arnhern, the Netherlands van Lauwe, B., International Institute of Tropical Agriculture, Miami, FL van  ...  ., University of Adelaide, Glen Osmond, Australia Stewart, B., Mississippi State University, MS Stewart, S., Mississippi State University, MS Stone, A.T., Johns Hopkins University, Baltimore, MD Stone,  ... 
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