E-MSD: the European Bioinformatics Institute Macromolecular Structure Database
Nucleic Acids ResearchPublished 1 January 2003Open access
Harry Boutselakis
Citations105
SJR quartileQ1
SJR score7.78
SNIP4.71
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TL;DR
The E-MSD macromolecular structure relational database is designed to be a single access point for protein and nucleic acid structures and related information, derived from Protein Data Bank entries.
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.
Keywords
Materials ScienceBiochemistry, Genetics and Molecular Biology
Nucleic Acids ResearchThe Protein Data Bank
39,839 Citations2000Helen M. Berman
The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource are described.
Acta Crystallographica Section D Biological CrystallographyThe CCP4 suite: programs for protein crystallography
17,277 Citations1994Number Collaborative Computational Project
The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography.
BiopolymersDictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
15,735 Citations1983Wolfgang Kabsch, Christian Sander
A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
Acta Crystallographica Section D Biological CrystallographyCrystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
15,734 Citations1998Axel T. Brünger, Paul D. Adams +12 more
The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement.
Acta Crystallographica Section D Biological CrystallographyRefinement of Macromolecular Structures by the Maximum-Likelihood Method
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In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up and new search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.
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Journal of Molecular BiologySCOP: A structural classification of proteins database for the investigation of sequences and structures
6,336 Citations1995Alexey G. Murzin, Steven E. Brenner +2 more
This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure and provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references.
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3,238 Citations1999Amos Bairoch, Rolf Apweiler
Current developments of the database include: cross-references to additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT.
Nucleic Acids ResearchThe SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
3,133 Citations2000Amos Bairoch
The Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT, is described.
StructureCATH – a hierarchic classification of protein domain structures
2,657 Citations1997CA Orengo, AD Michie +4 more
Analysis of the structural families generated by CATH reveals the prominent features of protein structure space and a database of well-characterised protein structure families will facilitate the assignment of structure-function/evolution relationships to both known and newly determined protein structures.
Journal of the ACMAn Algorithm for Subgraph Isomorphism
2,252 Citations1976J. R. Ullmann
A new algorithm is introduced that attains efficiency by inferentially eliminating successor nodes in the tree search by means of a brute-force tree-search enumeration procedure and a parallel asynchronous logic-in-memory implementation of a vital part of the algorithm is described.
Journal of Chemical Information and Computer SciencesSMILES. 2. Algorithm for generation of unique SMILES notation
1,268 Citations1989David Weininger, Arthur Weininger +1 more
Nucleic Acids ResearchThe PROSITE database, its status in 1999
1,100 Citations1999Kay Hofmann, Philip Bucher +2 more
Nucleic Acids ResearchThe InterPro database, an integrated documentation resource for protein families, domains and functional sites
1,091 Citations2001Rolf Apweiler
InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects.
Protein SciencePROMOTIF—A program to identify and analyze structural motifs in proteins
1,046 Citations1996E. Gail Hutchinson, Janet M. Thornton
A suite of programs, PROMOTIF, that analyzes a protein coordinate file and provides details about the structural motifs in the protein, and can also be used to compare motifS in a group of related structures, such as an ensemble of NMR structures.
Genome ResearchCreating the Gene Ontology Resource: Design and Implementation
963 Citations2001The Gene Ontology Consortium
The Gene Ontology project seeks to provide a set of structured vocabularies for specific biological domains that can be used to describe gene products in any organism, which includes building three extensive ontologies to describe molecular function, biological process, and cellular component.
The Mouseion at the JAXlibrary (Jackson Laboratory)Creating the gene ontology resource: design and implementation.
829 Citations2001Judith A. Blake, John Corradi +4 more
PubMed CentralThe Pfam Protein Families Database
770 Citations2002Bateman, Alex, Birney, Ewan +8 more
Journal of Chemical Information and Computer SciencesComparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures
629 Citations1994Jens Sadowski, Johann Gasteiger +1 more
Six currently available programs for automatic 3D structure generation were compared by converting the connectivity tables including appropriate stereodescriptors from this dataset of 639 molecular structures into 3D geometries: CONCORD, ALCOGEN, Chem-X, MOLGEO, COBRA, and CORINA.
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Trends in Biochemical SciencesPQS: a protein quaternary structure file server
540 Citations1998K. Henrick
A machine-readable list of the quaternary states for all nucleic acid and protein–nucleic acid complexes held in the PDB that was used in the annotation and checking stage described here is made available.
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515 Citations2002Dietmar Schomburg
The database is a resource for data of enzymes, classified according to the EC system of the IUBMB Enzyme Nomenclature Committee, and the entries are cross-referenced to other databases, i.e. organism classification, protein sequence, protein structure and literature references.
Journal of Molecular Graphics and ModellingVEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs
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The program VEGA is proposed, that was developed to create a bridge between the most popular molecular software packages, and some features are implemented some features to analyze, display and manage the three dimensional structure of the molecules.
PubMedThe ENZYME data bank.
343 Citations1994Amos Bairoch
The ENZYME data bank is a repository of information relative to the nomenclature of enzymes and contains the following data for each type of characterized enzyme: EC number Recommended name Alternative names Catalytic activity Cofactors (if any) Pointers to the SWISS-PROT protein sequence entrie(s) that correspond to the enzyme (if any)
Nucleic Acids ResearchThe EMBL data library
312 Citations1988Graham Cameron
The contents of the database, how it is available, and possible future enhancements of Data Library services are described.
Proteins Structure Function and BioinformaticsDiscriminating between homodimeric and monomeric proteins in the crystalline state
246 Citations2000Hannes Ponstingl, Kim Henrick +1 more
Trends in Biochemical SciencesRecent changes to RasMol, recombining the variants
229 Citations2000H. J. Bernstein, Herbert J. Bernstein
I would like to thank the many people who have contributed improvements, reported bugs and tested pre-releases of the RasMol 2.7 series releases.
Nucleic Acids ResearchProtein folds and families: sequence and structure alignments
202 Citations1999Liisa Holm, Christian Sander
Dali and HSSP are derived databases organizing protein space in the structurally known regions that provide a map of the currently known regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination.
Methods in enzymology on CD-ROM/Methods in enzymology[30] Macromolecular crystallographic information file
173 Citations1997Philip E. Bourne, Helen M. Berman +4 more
The Macromolecular Crystallographic Information File (mmCIF)
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Journal of Molecular Structure THEOCHEMWWW-based chemical information system
35 Citations1997Peter Ertl, Olivier Jacob
A WWW-based chemical information system developed within the Crop Protection Division of Novartis is presented, which enables easy retrieval of molecules from the corporate database, generation and editing of structures using a novel molecular editor written in Java.
Acta Crystallographica Section D Biological Crystallography<i>AutoDep</i>: a web-based system for deposition and validation of macromolecular structural information
15 Citations2000Dawei Lin, N. O. Manning +5 more
The design and full implementation of a new concept in data deposition and validation: AutoDep is described, which changes the traditional procedure for data acceptance and validation of the primary databases into an interactive depositor-driven operation which almost eliminates the delay between the acceptance of the data and its public release.