Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.

ABSTRACT: Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried

SUBMITTER: Thyme SB 

PROVIDER: S-EPMC3566986 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature