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Abstract
A key reason three-dimensional (3-D) protein structures are annotated with supporting or derived information is to understand the molecular basis of protein function. To this end, protein structure annotation databases curate key facts and observations, based on community-accepted standards, about the ~100,000 3-D experimental protein structures to date. This review will introduce the primary structure repositories, databases, and value-added structural annotation databases, as well as the range of information they provide. The different levels of annotation data (primary vs. derived vs. inferred) and how they should all be considered accordingly will also be described.
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Affiliation(s)
- Margaret J. Gabanyi
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Helen M. Berman
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
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2
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Rose PW, Prlić A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley SK. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res 2014; 43:D345-56. [PMID: 25428375 PMCID: PMC4383988 DOI: 10.1093/nar/gku1214] [Citation(s) in RCA: 367] [Impact Index Per Article: 36.7] [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: 12/19/2022] Open
Abstract
The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.
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Affiliation(s)
- Peter W Rose
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Andreas Prlić
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Chunxiao Bi
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Wolfgang F Bluhm
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Cole H Christie
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Shuchismita Dutta
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rachel Kramer Green
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - David S Goodsell
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - John D Westbrook
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jesse Woo
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Jasmine Young
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christine Zardecki
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Helen M Berman
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Philip E Bourne
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
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Young JY, Feng Z, Dimitropoulos D, Sala R, Westbrook J, Zhuravleva M, Shao C, Quesada M, Peisach E, Berman HM. Chemical annotation of small and peptide-like molecules at the Protein Data Bank. Database (Oxford) 2013; 2013:bat079. [PMID: 24291661 PMCID: PMC3843158 DOI: 10.1093/database/bat079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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. Database URL: http://wwpdb.org.
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Affiliation(s)
- Jasmine Y Young
- Department of Chemistry and Chemical Biology, and Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, 174 Frelinghuysen Rd, Piscataway, NJ 08854-8087, USA and San Diego Supercomputer Centre and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0743, USA
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Berman HM, Coimbatore Narayanan B, Di Costanzo L, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlić A, Rose PW, Shao C, Yang H, Young J, Zardecki C. Trendspotting in the Protein Data Bank. FEBS Lett 2013; 587:1036-45. [PMID: 23337870 PMCID: PMC4068610 DOI: 10.1016/j.febslet.2012.12.029] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [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: 11/15/2012] [Revised: 12/20/2012] [Accepted: 12/22/2012] [Indexed: 01/20/2023]
Abstract
The Protein Data Bank (PDB) was established in 1971 as a repository for the three dimensional structures of biological macromolecules. Since then, more than 85000 biological macromolecule structures have been determined and made available in the PDB archive. Through analysis of the corpus of data, it is possible to identify trends that can be used to inform us abou the future of structural biology and to plan the best ways to improve the management of the ever-growing amount of PDB data.
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Affiliation(s)
- Helen M Berman
- Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA.
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