Physics Commons^™

Modeling Correlated Main-Chain Motions In Proteins For Flexible Molecular Recognition., Maria Zavodsky, Ming Lei, M. Thorpe, Anthony Day, Leslie Kuhn

Anthony Roy Day

We describe a new method for modeling protein and ligand main-chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational space, including large-scale motions that typically cannot be reached in molecular dynamics simulations due to the computational intensity, as well as conformations that have not been observed yet by crystallography or NMR. A secondary goal is to assess the degree of flexibility consistent with protein–ligand recognition. Flexibility analysis of the target protein is performed using the graph-theoretic algorithm FIRST, which also identifies coupled networks of covalent and noncovalent bonds within the …