Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models

@article{citeulike:2209159, abstract = {The minimal requirements of a physics based potential that can refine protein structures is the existence of a correlation between the energy with native similarity and the scoring of the native structure as being lowest in energy. To develop such a force field, the relative weights of the Amber ff03 all-atom potential supplemented by an explicit hydrogen bond potential were adjusted by global optimization of energetic and structural criteria for a large set of protein decoys generated for a set of 58 nonhomologous proteins. The average correlation coefficient of the energy with TM-score significantly improved from 0.25 for the original ff03 potential to 0.65 for the optimized force field. The fraction of proteins for which the native structure had lowest energy increased from 0.22 to 0.90. Moreover, use of an explicit hydrogen bond potential improves scoring performance of the force field. Promising preliminary results were obtained in applying the optimized potentials to refine protein decoys using only an energy criterion to choose the best decoy among sampled structures. For a set of seven proteins, 63\% of the decoys improve, 18\% get worse, and 19\% are not changed. 10.1529/biophysj.107.121947}, author = {Wroblewska, Liliana and Jagielska, Anna and Skolnick, Jeffrey }, citeulike-article-id = {2209159}, doi = {10.1529/biophysj.107.121947}, journal = {Biophys. J.}, keywords = {forcefield}, month = {January}, pages = {biophysj.107.121947+}, posted-at = {2008-05-23 14:25:06}, priority = {2}, title = {Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models}, url = {http://dx.doi.org/10.1529/biophysj.107.121947}, year = {2008} }

TY - JOUR ID - citeulike:2209159 L3 - citeulike-article-id:2209159 TI - Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models JF - Biophys. J. SP - biophysj.107.121947 N2 - The minimal requirements of a physics based potential that can refine protein structures is the existence of a correlation between the energy with native similarity and the scoring of the native structure as being lowest in energy. To develop such a force field, the relative weights of the Amber ff03 all-atom potential supplemented by an explicit hydrogen bond potential were adjusted by global optimization of energetic and structural criteria for a large set of protein decoys generated for a set of 58 nonhomologous proteins. The average correlation coefficient of the energy with TM-score significantly improved from 0.25 for the original ff03 potential to 0.65 for the optimized force field. The fraction of proteins for which the native structure had lowest energy increased from 0.22 to 0.90. Moreover, use of an explicit hydrogen bond potential improves scoring performance of the force field. Promising preliminary results were obtained in applying the optimized potentials to refine protein decoys using only an energy criterion to choose the best decoy among sampled structures. For a set of seven proteins, 63% of the decoys improve, 18% get worse, and 19% are not changed. 10.1529/biophysj.107.121947 KW - forcefield AU - Wroblewska, Liliana AU - Jagielska, Anna AU - Skolnick, Jeffrey PY - 2008/01/04/ UR - http://dx.doi.org/10.1529/biophysj.107.121947 ER -