OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.

ABSTRACT: One of the many challenging tasks of protein design is the introduction of a completely new function into an existing protein scaffold. In this study, we introduce a new computational procedure OptGraft for placing a novel binding pocket onto a protein structure so as its geometry is minimally perturbed. This is accomplished by introducing a two-level procedure where we first identify where are the most appropriate locations to graft the new binding pocket into the protein fold by minimizing the departure from a set of geometric restraints using mixed-integer linear optimization. On identifying the suitable locations that can accommodate the new binding pocket, CHARMM energy calculations are employed to identify what mutations in the neighboring residues, if any, are needed to ensure that

SUBMITTER: Fazelinia H 

PROVIDER: S-EPMC2708043 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature