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Varadi M, Deshpande M, Nair S, Anyango S, Bertoni D, Velankar S. High-accuracy protein structure models in AlphaFold DB. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322093044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Velankar S, Kleywegt GJ. PDBe – bringing structure to biology. Acta Crystallogr A 2012. [DOI: 10.1107/s0108767312098285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Velankar S, Alhroub Y, Best C, Caboche S, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hendrickx PMS, Heuson E, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley R, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ. PDBe: Protein Data Bank in Europe. Nucleic Acids Res 2011; 40:D445-52. [PMID: 22110033 PMCID: PMC3245096 DOI: 10.1093/nar/gkr998] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
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 structure data, the PDB. In addition, PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community. Here we describe recently developed, extended or improved services, including an animated structure-presentation widget (PDBportfolio), a widget to graphically display the coverage of any UniProt sequence in the PDB (UniPDB), chemistry- and taxonomy-based PDB-archive browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well as validation and analysis results (Vivaldi).
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Affiliation(s)
- S Velankar
- Protein Data Bank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Quesada M, Westbrook J, Oldfield T, Young J, Swaminathan J, Feng Z, Velankar S, Matsuura T, Ulrich E, Madding S, Kleywegt GJ, Markley JL, Nakamura H, Berman HM. The wwPDB common tool for deposition and annotation. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311089896] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ. PDBe: Protein Data Bank in Europe. Nucleic Acids Res 2009; 38:D308-17. [PMID: 19858099 PMCID: PMC2808887 DOI: 10.1093/nar/gkp916] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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). PDBe also works closely with its collaborators at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new database infrastructure based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple textual queries or more complex 3D structure-based queries. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.
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Affiliation(s)
- S Velankar
- Protein Databank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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Sen S, Van Ginkel G, Kapopoulou A, Sahni G, Swaminathan GJ, Newman RH, Velankar S, Henrick K. Autodep 4.1: a web-based deposition and archival system. Acta Crystallogr A 2007. [DOI: 10.1107/s0108767307096882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Swaminathan GJ, Velankar S, Newman RH, Kapopoulou A, Henrick K. AutoDep 4.0: a web-based deposition and archival system. Acta Crystallogr A 2006. [DOI: 10.1107/s0108767306099697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Tagari M, Tate J, Swaminathan GJ, Newman R, Naim A, Vranken W, Kapopoulou A, Hussain A, Fillon J, Henrick K, Velankar S. E-MSD: improving data deposition and structure quality. Nucleic Acids Res 2006; 34:D287-90. [PMID: 16381867 PMCID: PMC1347525 DOI: 10.1093/nar/gkj163] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458-462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - S. Velankar
- To whom correspondence should be addressed. Tel: +44 1223 494 646; Fax: +44 1223 494 468;
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Affiliation(s)
- J. Martin
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - S. Velankar
- Department of Chemical Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
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Swaminathan GJ, Velankar S, McNeil P, Suarez A, Barrell D, Jacobsen J, Henrick K. Structure integration with function, taxonomy and sequences (SIFTS). Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305095371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R. SOAP-based services provided by the European Bioinformatics Institute. Nucleic Acids Res 2005; 33:W25-8. [PMID: 15980463 PMCID: PMC1160251 DOI: 10.1093/nar/gki491] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
SOAP (Simple Object Access Protocol) () based Web Services technology () has gained much attention as an open standard enabling interoperability among applications across heterogeneous architectures and different networks. The European Bioinformatics Institute (EBI) is using this technology to provide robust data retrieval and data analysis mechanisms to the scientific community and to enhance utilization of the biological resources it already provides [N. Harte, V. Silventoinen, E. Quevillon, S. Robinson, K. Kallio, X. Fustero, P. Patel, P. Jokinen and R. Lopez (2004) Nucleic Acids Res., 32, 3–9]. These services are available free to all users from .
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - R. Lopez
- To whom correspondence should be addressed at: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 ISD, UK. Tel: +44 1223 494423; Fax: +44 1223 494468;
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Abstract
The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the ‘Structure Integration with Function, Taxonomy and Sequences (SIFTS)’ initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.
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Affiliation(s)
- S Velankar
- Macromolecular Structure Database Group (E-MSD), EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Golovin A, Oldfield TJ, Tate JG, Velankar S, Barton GJ, Boutselakis H, Dimitropoulos D, Fillon J, Hussain A, Ionides JMC, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Pajon A, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan GJ, Tagari M, Tromm S, Vranken W, Henrick K. E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res 2004; 32:D211-6. [PMID: 14681397 PMCID: PMC308812 DOI: 10.1093/nar/gkh078] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).
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Affiliation(s)
- A Golovin
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Boutselakis H, Dimitropoulos D, Fillon J, Golovin A, Henrick K, Hussain A, Ionides J, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Oldfield T, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan J, Tagari M, Tate J, Tromm S, Velankar S, Vranken W. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res 2003; 31:458-62. [PMID: 12520052 PMCID: PMC165512 DOI: 10.1093/nar/gkg065] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2002] [Accepted: 10/03/2002] [Indexed: 11/14/2022] Open
Abstract
The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.
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Affiliation(s)
- H Boutselakis
- EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Henrick K, Boutselakis H, Dimitropoulos D, Golovin A, Ionides J, John M, Keller P, Krissinel E, Mcneil P, Pineda J, Sobhany S, Tate J, Suarez-Uruena A, Velankar S. The EBI macromolecular structure database (E-MSD) and structural genomics. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302087081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Henrick K, Dimitropoulos D, Keller P, Ionides J, Krissinel E, Velankar S, Boutselakis H, McNeil P, Golovin A, Pineda J. The European Bioinformatics Institute Macromolecular Structure Database (E-MSD). Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302093546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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