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Generation of pseudonative protein structures for threading
Author(s) -
Hamprecht Fred A.,
Scott Walter,
van Gunsteren Wilfred F.
Publication year - 1997
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199708)28:4<522::aid-prot6>3.0.co;2-b
Subject(s) - threading (protein sequence) , template , protein structure prediction , computer science , protein structure , nanotechnology , materials science , chemistry , biochemistry
The threading approach to protein structure prediction suffers from the limited number of substantially different folds available as templates. A method is presented for the generation of artificial protein structures, amenable to threading, by modification of native ones. The artificial structures so generated are compared to the native ones and it is shown that, within the accuracy of the pseudoenergy function or force field used, these two types of structures appear equally useful for threading. Since a multitude of pseudonative artificial structures can be generated per native structure, the pool of pseudonative template structures for threading can be enormously enlarged by the inclusion of the pseudonative artificial structures. Proteins 28:522–529, 1997. © 1997 Wiley‐Liss, Inc.