Literature DB >> 9399863

Touring protein fold space with Dali/FSSP.

L Holm1, C Sander.   

Abstract

The FSSP database and its new supplement, the Dali Domain Dictionary, present a continuously updated classification of all known 3D protein structures. The classification is derived using an automatic structure alignment program (Dali) for the all-against-all comparison of structures in the Protein Data Bank. From the resulting enumeration of structural neighbours (which form a surprisingly continuous distribution in fold space) we derive a discrete fold classification in three steps: (i) sequence-related families are covered by a representative set of protein chains; (ii) protein chains are decomposed into structural domains based on the recurrence of structural motifs; (iii) folds are defined as tight clusters of domains in fold space. The fold classification, domain definitions and test sets for sequence-structure alignment (threading) are accessible on the web at www.embl-ebi.ac.uk/dali . The web interface provides a rich network of links between neighbours in fold space, between domains and proteins, and between structures and sequences leading, for example, to a database of explicit multiple alignments of protein families in the twilight zone of sequence similarity. The Dali/FSSP organization of protein structures provides 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.

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Year:  1998        PMID: 9399863      PMCID: PMC147193          DOI: 10.1093/nar/26.1.316

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  16 in total

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Authors:  C Sander; R Schneider
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Authors:  A Bairoch
Journal:  Nucleic Acids Res       Date:  1992-05-11       Impact factor: 16.971

3.  A database of protein structure families with common folding motifs.

Authors:  L Holm; C Ouzounis; C Sander; G Tuparev; G Vriend
Journal:  Protein Sci       Date:  1992-12       Impact factor: 6.725

4.  SRS: information retrieval system for molecular biology data banks.

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Review 5.  Mapping the protein universe.

Authors:  L Holm; C Sander
Journal:  Science       Date:  1996-08-02       Impact factor: 47.728

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Authors:  J F Gibrat; T Madej; S H Bryant
Journal:  Curr Opin Struct Biol       Date:  1996-06       Impact factor: 6.809

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Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

8.  SCOP: a structural classification of proteins database for the investigation of sequences and structures.

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9.  Identification and analysis of domains in proteins.

Authors:  S A Islam; J Luo; M J Sternberg
Journal:  Protein Eng       Date:  1995-06

10.  Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions.

Authors:  A S Siddiqui; G J Barton
Journal:  Protein Sci       Date:  1995-05       Impact factor: 6.725

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  213 in total

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Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

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Journal:  Protein Sci       Date:  1999-08       Impact factor: 6.725

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Journal:  Protein Sci       Date:  2000-12       Impact factor: 6.725

8.  Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.

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Journal:  EMBO J       Date:  2000-08-15       Impact factor: 11.598

9.  A sequence and structural study of transmembrane helices.

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10.  Enhanced protein fold recognition using secondary structure information from NMR.

Authors:  D J Ayers; P R Gooley; A Widmer-Cooper; A E Torda
Journal:  Protein Sci       Date:  1999-05       Impact factor: 6.725

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