A computer system to perform structure comparison using TOPS representations of protein structure

We describe the design and implementation of a fast topology-based method for protein structure comparison. The approach uses the TOPS topological representation of protein structure, aligning two structures using a common discovered pattern and generating measure of distance derived from an insert...

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Bibliographic Details
Published inComputers & chemistry Vol. 26; no. 1; pp. 23 - 30
Main Authors Gilbert, David, Westhead, David, Viksna, Juris, Thornton, Janet
Format Journal Article
LanguageEnglish
Published England Elsevier Ltd 01.12.2001
Subjects
Algorithms
Artificial Intelligence
Constraints
Molecular Structure
Pattern discovery
Pattern matching
Pattern Recognition, Automated
Protein motifs
Protein topology
Proteins - chemistry
Sequence Homology
Software
Structure comparison
Protein topology
Constraints
Pattern discovery
Structure comparison
Pattern matching
Protein motifs
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Summary:We describe the design and implementation of a fast topology-based method for protein structure comparison. The approach uses the TOPS topological representation of protein structure, aligning two structures using a common discovered pattern and generating measure of distance derived from an insert score. Heavy use is made of a constraint-based pattern-matching algorithm for TOPS diagrams that we have designed and described elsewhere (Bioinformatics 15(4) (1999) 317). The comparison system is maintained at the European Bioinformatics Institute and is available over the Web at tops.ebi.ac.uk/tops. Users submit a structure description in Protein Data Bank (PDB) format and can compare it with structures in the entire PDB or a representative subset of protein domains, receiving the results by email.
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ISSN:0097-8485
DOI:10.1016/S0097-8485(01)00096-1