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A procedure for the automatic determination of hydrophobic cores in protein structures
Author(s) -
Swindells Mark B.
Publication year - 1995
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 - 10.1002/pro.5560040112
Subject(s) - side chain , protein secondary structure , topology (electrical circuits) , sequence (biology) , core (optical fiber) , network topology , protein structure , computer science , biological system , chemistry , chain (unit) , crystallography , algorithm , physics , biology , mathematics , biochemistry , combinatorics , organic chemistry , polymer , telecommunications , operating system , astronomy
An algorithm is described for automatically detecting hydrophobic cores in proteins of known structure. Three pieces of information are considered in order to achieve this goal. These are: secondary structure, side‐chain accessibility, and side‐chain‐side‐chain contacts. Residues are considered to contribute to a core when they occur in regular secondary structure and have buried side chains that form predominantly nonpolar contacts with one another. This paper describes the algorithm's application to families of proteins with conserved topologies but low sequence similarities. The aim of this investigation is to determine the efficacy of the algorithm as well as to study the extent to which similar cores are identified within a common topology.