Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling.

ABSTRACT: The OPLS-AA all-atom force field and the Analytical Generalized Born plus Non-Polar (AGBNP) implicit solvent model, in conjunction with torsion angle conformational search protocols based on the Protein Local Optimization Program (PLOP), are shown to be effective in predicting the native conformations of 57 9-residue and 35 13-residue loops of a diverse series of proteins with low sequence identity. The novel nonpolar solvation free energy estimator implemented in AGBNP augmented by correction terms aimed at reducing the occurrence of ion pairing are important to achieve the best prediction accuracy. Extended versions of the previously developed PLOP-based conformational search schemes based on calculations in the crystal environment are reported that are suitable for application to loop h

SUBMITTER: Felts AK 

PROVIDER: S-EPMC2533438 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature