Summary: proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS
Development of a new physics-based internal
coordinate mechanics force field and its
application to protein loop modeling
Yelena A. Arnautova, Ruben A. Abagyan, and Maxim Totrov*
Molsoft L.L.C., 3366 North Torrey Pines Court, Suite 300, La Jolla, California 92037
INTRODUCTION
All-atom force fields represent a very important tool used for
theoretical studies of biomolecular systems. They are essential for
many areas of computational chemistry including the prediction of
protein structure and function, the study of protein­protein inter-
actions, and the prediction of structure and binding affinities of
protein­ligand complexes. Although the large size of conforma-
tional space and the complexity of the energy landscapes make
protein structure prediction using all-atom force-fields prohibitive
for all but smallest proteins and peptides, all-atom force fields are
emerging as a major tool for the refinement of protein models
generated using comparative modeling methods.
Although modern comparative modeling methods are able to
produce models resembling closely the native conformation when

Source: Abagyan, Ruben - School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego

Collections: Biology and Medicine