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Protein structural topology: Automated analysis and diagrammatic representation
Author(s) -
Westhead David R.,
Slidel Timothy W.F.,
Flores Tomas P.J.,
Thornton Janet M.
Publication year - 1999
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.8.4.897
Subject(s) - diagrammatic reasoning , topology (electrical circuits) , computer science , representation (politics) , fold (higher order function) , sequence (biology) , diagram , algorithm , theoretical computer science , mathematics , combinatorics , biology , database , politics , political science , law , genetics , programming language
The topology of a protein structure is a highly simplified description of its fold including only the sequence of secondary structure elements, and their relative spatial positions and approximate orientations. This information can be embodied in a two‐dimensional diagram of protein topology, called a TOPS cartoon. These cartoons are useful for the understanding of particular folds and making comparisons between folds. Here we describe a new algorithm for the production of TOPS cartoons, which is more robust than those previously available, and has a much higher success rate. This algorithm has been used to produce a database of protein topology cartoons that covers most of the data bank of known protein structures.