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BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions.

We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems.

Pubmed ID: 18288446 RIS Download

Mesh terms: Automatic Data Processing | Computer-Assisted Instruction | Databases, Protein | Nuclear Magnetic Resonance, Biomolecular | Protein Conformation | Research Design

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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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European Bioinformatics Institute

A non-profit academic organization for research and services in bioinformatics that provides freely available data from life science experiments, performs basic research in computational biology, and offers an extensive user training programme, supporting researchers in academia and industry. The Institute manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures.

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Worldwide Protein Data Bank

A free and public single global PDB archive of macromolecular structural data overseen by organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). This site provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.

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Cambridge Structural Data Base

It records bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds whose 3D structures have been determined using X-ray diffraction and neutron diffraction.
The CSD records results of single crystal studies and powder diffraction studies which yield 3D atomic coordinate data for at least all non-H atoms. In some cases the CCDC is unable to obtain coordinates, and incomplete entries are archived to the CSD.
The CSD includes crystal structure data arising from:
* publications in the open literature
* Private Communications to the CSD (via direct data deposition)
The Cambridge Structural Database System (CSDS) is a single product that comprises the following components: The Cambridge Structural Database (CSD); CSDS Software: search and information retrieval (ConQuest), structure visualization (Mercury), statistical analysis of retrieved data (VISTA), and software for database creation (PreQuest); Knowledge bases derived from the CSD: Mogul (intramolecular geometry) and IsoStar (intermolecular interactions, including data from the PDB).
Cambridge Structural Database (CSD) is the world repository of small-molecule crystal structures. For example, the crystal structures supported by the National Institute on Drug Abuse are deposited here.

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PDBj - Protein Data Bank Japan

PDBj (Protein Data Bank Japan) maintains a centralized PDB archive of macromolecular structures and provides integrated tools, in collaboration with the RCSB, the BMRB in USA and the PDBe in EU.

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Human Metabolome Database

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data. The database contains over 6500 metabolite entries including both water-soluble and lipid soluble metabolites as well as metabolites that would be regarded as either abundant (> 1 uM) or relatively rare (< 1 nM). Additionally, approximately 1500 protein (and DNA) sequences are linked to these metabolite entries. Each MetaboCard entry contains more than 100 data fields with 2/3 of the information being devoted to chemical/clinical data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank) and a variety of structure and pathway viewing applets. The HMDB database supports extensive text, sequence, chemical structure and relational query searches. Two additional databases, DrugBank and FooDB are also part of the HMDB suite of databases. DrugBank contains equivalent information on ~1500 drugs while FooDB contains equivalent information on ~2000 food components and food additives. The simple text query supports general text queries of the entire textual component of the database. Clicking on the Browse button generates a tabular synopsis of the HMDB''s content. This browse view allows users to casually scroll through the database or re-sort its contents. Clicking on a given MetaboCard button brings up the full data content for the corresponding metabolite. The Biofluids button generates hyperlinked tables listing normal and abnormal concentrations of different metabolites for 7 different biofluids. The ChemQuery button allows users to draw or write a chemical compound and to search HMDB for chemicals similar or identical to the query compound. The TextQuery button supports a more sophisticated text search of the text portion of HMDB. The SeqSearch button allows users to conduct BLAST sequence searches of the 5500 sequences contained in HMDB. Both single and multiple sequence BLAST queries are supported. The DataExtractor button opens an easy-to-use relational query search tool that allows users to select or search over various combinations of subfields. The DataExtractor is the most sophisticated search tool for HMDB. The MS Search allows users to submit Mass spectral files (MoverZ format) that will be searched against the HMDB''s library of MS/MS spectra. This allows the identification of metabolites from mixtures via MS/MS spectroscopy. The NMR Search allows users to submit peak lists from 1H or 13C NMR spectra (both pure and mixtures) and to have these peak lists compared to the NMR libraries contained in the HMDB. This allows the identification of metabolites from mixtures via NMR spectroscopy. The Download button provides links to collected sequence, image and text files associated with the HMDB. The HML Home button links to the Human Metabolome Library (HML) home page. The HML lists metabolites that can be ordered for a fee by researchers around the world. The Explain button lists statistics and source data used to assemble the HMDB. Sponsors: This project is supported by Genome Alberta & Genome Canada, a not-for-profit organization that is leading Canada''s national genomics strategy with $600 million in funding from the federal government.

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