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PEPCAT—A new tool for conformational analysis of peptides
Author(s) -
O'Donohue M. F.,
Minasian E.,
Leach S. J.,
Burgess A. W.,
Treutlein H. R.
Publication year - 2000
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(20000430)21:6<446::aid-jcc4>3.0.co;2-s
Subject(s) - chemistry , pentapeptide repeat , peptide , molecular dynamics , computer science , computational biology , computational chemistry , biochemistry , biology
We report a new technique for the efficient analysis and visualization of peptide and protein conformations and conformational relationships, which we have implemented in a computer program called PEPCAT. PEPCAT (an abbreviation for Peptide Conformational Analysis Tool) provides a simple, graphical, and flexible framework that allows the user to define a specific structural feature or juxtaposition of amino acids and to follow the fate of the motif during a molecular dynamics simulation. Here we describe the PEPCAT analysis of the effects of environmental and chemical modifications on conformational preferences of a regulator of hemopoiesis, namely the pentapeptide pyro‐EEDCK, and of a conformational transition in the immunosuppressant drug cyclosporin A. PEPCAT, however, can be applied to the conformational analysis of peptides and proteins in general. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 446–461, 2000