✦ LIBER ✦

Structure-based design of model proteins

✍ Scribed by Jayanth R. Banavar; Marek Cieplak; Amos Maritan; Gautham Nadig; Flavio Seno; Saraswathi Vishveshwara

Publisher: John Wiley and Sons
Year: 1998
Tongue: English
Weight: 117 KB
Volume: 31
Category: Article
ISSN: 0887-3585
DOI: 10.1002/(sici)1097-0134(19980401)31:1<10::aid-prot2>3.0.co;2-l

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✦ Synopsis

A structure-based, sequencedesign procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native state. The procedure allows the design of sequences with large and small stability gaps in a randombond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact energies to both the native and nonnative contacts. The design procedure is also successfully applied to the two-dimensional HP model. Proteins 31:10-20, 1998.

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