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Predicting conformational switches in proteins
Author(s) -
Young Malin,
Kirshenbaum Kent,
Dill Ken A.,
Highsmith Stefan
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.8.9.1752
Subject(s) - ambivalence , protein structure , function (biology) , computational biology , set (abstract data type) , protein function , protein design , chemistry , biology , computer science , genetics , biochemistry , psychology , programming language , social psychology , gene
We describe a new computational technique to predict conformationally switching elements in proteins from their amino acid sequences. The method, called ASP (Ambivalent Structure Predictor), analyzes results from a secondary structure prediction algorithm to identify regions of conformational ambivalence. ASP identifies ambivalent regions in 16 test protein sequences for which function involves substantial backbone rearrangements. In the test set, all sites previously described as conformational switches are correctly predicted to be structurally ambivalent regions. No such regions are predicted in three negative control protein sequences. ASP may be useful as a guide for experimental studies on protein function and motion in the absence of detailed three‐dimensional structural data.