IPRO: an iterative computational protein library redesign and optimization procedure.

ABSTRACT: A number of computational approaches have been developed to reengineer promising chimeric proteins one at a time through targeted point mutations. In this article, we introduce the computational procedure IPRO (iterative protein redesign and optimization procedure) for the redesign of an entire combinatorial protein library in one step using energy-based scoring functions. IPRO relies on identifying mutations in the parental sequences, which when propagated downstream in the combinatorial library, improve the average quality of the library (e.g., stability, binding affinity, specific activity, etc.). Residue and rotamer design choices are driven by a globally convergent mixed-integer linear programming formulation. Unlike many of the available computational approaches, the procedure allows

SUBMITTER: Saraf MC 

PROVIDER: S-EPMC1459523 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature