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The RCSB Protein Data Bank: redesigned web site and web services.

Nucleic acids research | Jan 23, 2011

The RCSB Protein Data Bank (RCSB PDB) web site ( has been redesigned to increase usability and to cater to a larger and more diverse user base. This article describes key enhancements and new features that fall into the following categories: (i) query and analysis tools for chemical structure searching, query refinement, tabulation and export of query results; (ii) web site customization and new structure alerts; (iii) pair-wise and representative protein structure alignments; (iv) visualization of large assemblies; (v) integration of structural data with the open access literature and binding affinity data; and (vi) web services and web widgets to facilitate integration of PDB data and tools with other resources. These improvements enable a range of new possibilities to analyze and understand structure data. The next generation of the RCSB PDB web site, as described here, provides a rich resource for research and education.

Pubmed ID: 21036868 RIS Download

Mesh terms: Animals | Computer Graphics | Databases, Protein | Humans | Internet | Ligands | Mice | Protein Conformation | Proteins | Systems Integration | User-Computer Interface

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This is a list of tools and resources that we have found mentioned in this publication.

Biological Magnetic Resonance Data Bank

Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance (NMR) spectroscopic investigations of biological macromolecules and metabolites. BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR. The BMRB archive consists of four main data depositories: quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors and derived data; databases for NMR restraints processed from original author depositions available from the Protein Data Bank; time-domain spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules; and a database of one- and two-dimensional (1)H and (13)C one- and two-dimensional NMR spectra for over 250 metabolites. BMRB has tools for querying the archive and retrieving information and an ftp site where data in the archive can be downloaded in bulk. BMRB accepts quantitative NMR data for a peptide, protein, nucleic acid, or polysaccharide and their ligands and cofactors assigned on an atom-specific basis, and data derived from the analysis of such data.


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A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world''''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.


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Enzyme Nomenclature

Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes by the reactions they catalyze. Also included are links to individual documents and advice is provided on how to suggest new enzymes for listing, or correction of existing entries. The common names of all listed enzymes are listed, along with their EC numbers. Where an enzyme has been deleted or transferred to another EC number, this information is also indicated. Each list is linked to either separate entries for each entry or to files with up to 50 enzymes in each file. A start has been made in showing the pathways in which enzymes participate. For other enzymes a glossary entry has been added which may be just a systematic name or a link to a graphic representation. The glossary from Enzyme Nomenclature, 1992 may also be consulted. This has been updated with subsequent glossary entries. Each enzyme entry has links to other databases. Enzyme Subclasses provide links to a list of sub-subclasses which in turn list the enzymes linked to separate files for each enzyme, or to a list as part of a file with up to 50 enzymes per file.


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