Energy Minimization of Discrete Protein Titration State Models Using Graph Theory.

ABSTRACT: There are several applications in computational biophysics that require the optimization of discrete interacting states, for example, amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of "maximum flow-minimum cut" graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is tran

SUBMITTER: Purvine E 

PROVIDER: S-EPMC5001885 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature