A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins.

ABSTRACT: A coarse-grained potential for protein simulations and fold ranking is presented. The potential is based on a two-point model of individual amino acids and a specific implementation of hydrogen bonding. Parameters are determined for distance dependent pair interactions, pseudo bonds, angles, and torsions. A scaling factor for a hydrogen bonding term is also determined. Iterative sampling for 4867 proteins reproduces distributions of internal coordinates and distances observed in the Protein Data Bank. The adjustment of the potential and resampling are in the spirit of the generalized ensemble approach. No native structure information (e.g., secondary structure) is used in the calculation of the potential or in the simulation of a particular protein. The potential is subject to two tests as

SUBMITTER: Majek P 

PROVIDER: S-EPMC2719022 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature