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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  ...  PDBe also develops tools that help the biomedical science community to make effective use of the data in the PDB and EMDB for their research.  ...  ACKNOWLEDGEMENTS The authors would like to thank all collaborators and partners in the EBI, EMBL, wwPDB, EMDataBank, BioMagResBank, CCPN, CCP4, CCDC and other collaborative efforts.  ... 
doi:10.1093/nar/gkt1180 pmid:24288376 pmcid:PMC3965016 fatcat:rv2cpebl5ffzbdppo654oahfly

PDBe: Protein Data Bank in Europe

S. Velankar, Y. Alhroub, A. Alili, C. Best, H. C. Boutselakis, S. Caboche, M. J. Conroy, J. M. Dana, G. van Ginkel, A. Golovin, S. P. Gore, A. Gutmanas (+21 others)
2010 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank  ...  PDBe also develops new tools to make structural data more widely and more easily available to the biomedical community.  ...  depositing their structures and experimental data in the PDB and EMDB.  ... 
doi:10.1093/nar/gkq985 pmid:21045060 pmcid:PMC3013808 fatcat:732ckrjoq5afnk3jt2i7jwjcvy

PDBe: Protein Data Bank in Europe

S. Velankar, Y. Alhroub, C. Best, S. Caboche, M. J. Conroy, J. M. Dana, M. A. Fernandez Montecelo, G. van Ginkel, A. Golovin, S. P. Gore, A. Gutmanas, P. Haslam (+20 others)
2011 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved in managing the single global archive of biomacromolecular  ...  In addition, PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community.  ...  for depositing its structures and experimental data in the PDB, BMRB and EMDB.  ... 
doi:10.1093/nar/gkr998 pmid:22110033 pmcid:PMC3245096 fatcat:q5b4mmkggbepdebpme7koi7hye

PDBe: Protein Data Bank in Europe

S. Velankar, C. Best, B. Beuth, C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman (+13 others)
2009 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe) (http://www .ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international archive  ...  of bio-macromolecular structure data, the Protein Data Bank (PDB).  ...  ACKNOWLEDGEMENTS We wish to thank all collaborators and partners in the EBI, EMBL, wwPDB and other collaborative efforts, as  ... 
doi:10.1093/nar/gkp916 pmid:19858099 pmcid:PMC2808887 fatcat:amgz3equ6jgenhym77vbghy47e

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

Saqib Mir, Younes Alhroub, Stephen Anyango, David R Armstrong, John M Berrisford, Alice R Clark, Matthew J Conroy, Jose M Dana, Mandar Deshpande, Deepti Gupta, Aleksandras Gutmanas, Pauline Haslam (+10 others)
2017 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data.  ...  This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability.  ...  The Protein Data Bank in Europe (PDBe; pdbe.org; (2) ) is a founding member of the Worldwide Protein Data Bank (wwPDB; http://wwpdb.org (3)), the inter-national consortium that manages the PDB archive  ... 
doi:10.1093/nar/gkx1070 pmid:29126160 pmcid:PMC5753225 fatcat:j6ocp5cauvau3d7jd4gw3htwiq

The Protein Data Bank in Europe (PDBe): bringing structure to biology

Sameer Velankar, Gerard J. Kleywegt
2011 Acta Crystallographica Section D: Biological Crystallography  
Introduction The Protein Data Bank in Europe (PDBe; http://pdbe.org; Velankar et al., 2010 Velankar et al., , 2011 , previously known as the European Macromolecular Structure Database (MSD; Velankar  ...  et al., 2005; Tagari et al., 2006) , is the European partner in the Worldwide Protein Data Bank (wwPDB; http:// wwpdb.org; Berman et al., 2007) .  ... 
doi:10.1107/s090744491004117x pmid:21460450 pmcid:PMC3069747 fatcat:gpse5hxwwvbyxbqhrrsodahkye

Enhancing small-molecule information in the Protein Data Bank in Europe

Lukáš Pravda, The PDBe
2019 Acta Crystallographica Section A: Foundations and Advances  
As part of the data enrichment process in the Protein Data Bank in Europe [1] we have extended small molecule information to include scaffolds, fragments, physicochemical properties, and 2D coordinates  ...  Interaction information between macromolecules and small molecules is already available through the new aggregated views for proteins [2] which are part of the Protein Data Bank in Europe Knowledge Base  ...  As part of the data enrichment process in the Protein Data Bank in Europe [1] we have extended small molecule information to include scaffolds, fragments, physicochemical properties, and 2D coordinates  ... 
doi:10.1107/s2053273319093707 fatcat:juao2qiysndzffkqkeop3lpwmu

PDBe – bringing structure to biology

S. Velankar, G. J. Kleywegt
2012 Acta Crystallographica Section A Foundations of Crystallography  
in the gas phase.  ...  In both cases, though, both BP and CB can adopt higher-energy planar conformations in some crystal structures.  ...  EMBL-EBI's Protein Data Bank in Europe (PDBe; pdbe.org) [1, 2] , one of the founders of the Worldwide Protein Data Bank (wwPDB; wwpdb.org), is committed to becoming such a resource.  ... 
doi:10.1107/s0108767312098285 fatcat:r6cmjcrq3vgxfoboyzfigctdsy

PDBe: bringing structure to biology and beyond

Matthew J. Conroy, Sameer Velankar
2017 Acta Crystallographica Section A: Foundations and Advances  
Protein Data Bank in Europe (PDBe) [1] a founder member of the wwPDB, has a mission to bring structure to biology.  ...  In conjunction with Europe PMC [3], PDBe is able to display figures and legends from open-access publications describing PDB entries and datamine literature for instances of PDB codes.  ...  Protein Data Bank in Europe (PDBe) [1] a founder member of the wwPDB, has a mission to bring structure to biology.  ... 
doi:10.1107/s2053273317089963 fatcat:q2gizjtqcvbilftnqj7ikiozcq

PDBe: improved findability of macromolecular structure data in the PDB

2019 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe), a founding member of the Worldwide Protein Data Bank (wwPDB), actively participates in the deposition, curation, validation, archiving and dissemination of macromolecular  ...  PDBe supports diverse research communities in their use of macromolecular structures by enriching the PDB data and by providing advanced tools and services for effective data access, visualization and  ...  INTRODUCTION Protein Data Bank in Europe (PDBe; pdbe.org) is a founding member of the Worldwide Protein Data Bank (ww-PDB; wwpdb.org) (1), the international consortium responsible for the management of  ... 
doi:10.1093/nar/gkz990 pmid:31691821 pmcid:PMC7145656 fatcat:vi6couzcmrbzfkt4gml4o2zyiq

PDBe-KB: a community-driven resource for structural and functional annotations

Mihaly Varadi, PDBe-KB Consortium
2021 Acta Crystallographica Section A: Foundations and Advances  
The Protein Data Bank in Europe -Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative data resource that provides literature-derived, curated and predicted structural and  ...  functional annotations of molecular structure data [1].  ...  /pdbe-kb/protein/P0DTC2).  ... 
doi:10.1107/s0108767321090024 fatcat:j3onl6osbzbgbawaid5m7ggftu

PDBe-KB: a community-driven resource for structural and functional annotations

2019 Nucleic Acids Research  
The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural  ...  and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB).  ...  ACKNOWLEDGEMENTS We would like to thank all the members of PDBe team for their continued support of the design and development of PDBe-KB.  ... 
doi:10.1093/nar/gkz853 pmid:31584092 pmcid:PMC6943075 fatcat:lbpb4ss3ynaetnusqksvrbjy6y

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  ...  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  ...  INTRODUCTION The Protein Data Bank in Europe (PDBe; http://pdbe.org; 1) is actively involved in managing three core archives in molecular and cellular structural biology.  ... 
doi:10.1093/nar/gkv1047 pmid:26476444 pmcid:PMC4702783 fatcat:sqjtb2p3drbjncdycqrfr3m2lm

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  
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  ...  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.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided  ... 
doi:10.1007/s10858-010-9439-3 pmid:20680401 pmcid:PMC2950272 fatcat:dwh4dfnbavfvdgsnvgp3pemj34

PDBe-KB: collaboratively defining the biological context of structural data

PDBe-KB consortium
2021
The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations  ...  derived from or relevant to the Protein Data Bank (PDB).  ...  In addition, we thank the consortium members and the users of PDBe-KB, who continuously provide suggestions and feedback on how to improve our services.  ... 
doi:10.1093/nar/gkab988 pmid:34755867 pmcid:PMC8728252 fatcat:fsl366s2jfdobge6gvqctu4zva
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