Optimization of van der Waals energy for protein side-chain placement and design.

ABSTRACT: Computational determination of optimal side-chain conformations in protein structures has been a long-standing and challenging problem. Solving this problem is important for many applications including homology modeling, protein docking, and for placing small molecule ligands on protein-binding sites. Programs available as of this writing are very fast and reasonably accurate, as measured by deviations of side-chain dihedral angles; however, often due to multiple atomic clashes, they produce structures with high positive energies. This is problematic in applications where the energy values are important, for example when placing small molecules in docking applications; the relatively small binding energy of the small molecule is drowned by the large energy due to atomic clashes that hamper

SUBMITTER: Fahmy A 

PROVIDER: S-EPMC3183803 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature