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Design of proteins with hydrophobic and polar amino acids
Author(s) -
Micheletti Cristian,
Seno Flavio,
Maritan Amos,
Banavar Jayanth R.
Publication year - 1998
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(19980701)32:1<80::aid-prot9>3.0.co;2-i
Subject(s) - amino acid , granularity , protein design , chemistry , lattice protein , alanine , polar , amino acid residue , biological system , protein structure , stereochemistry , computational biology , biochemistry , peptide sequence , computer science , biology , physics , astronomy , gene , operating system
A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of 20 single chain proteins. Strikingly, the percentage of successful identification of the nature of the residues benchmarked against naturally occurring proteins and their homologues is around 75%, independent of the complexity of the design procedure. Typically, the lowest success rate occurs for residues such as alanine that have a high secondary structure functionality. Using a simple lattice model, we argue that one possible shortcoming of the model studied may involve the coarse‐graining of the 20 kinds of amino acids into just two effective types. Proteins 32:80–87, 1998. © 1998 Wiley‐Liss, Inc.