A new pairwise folding potential based on improved decoy generation and side-chain packing.

@article{citeulike:2931886, abstract = {A new force field for pairwise residue interactions as a function of C(alpha) to C(alpha) distances is presented. The force field was developed through the solution of a linear programming formulation with large sets of constraints. The constraints are based on the construction of >80,000 low-energy decoys for a set of proteins and requiring the decoy energies for each protein system to be higher than the native conformation of that particular protein. The generation of a robust force field was facilitated by the use of a novel decoy generation process, which involved the rational selection of proteins to add to the training set and included a significant energy minimization of the decoys. The force field was tested on a large set of decoys for various proteins not included in the training set and shown to perform well compared with a leading force field in identifying the native conformation for these proteins.}, address = {Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08540, USA.}, author = {Loose, C. and Klepeis, J. L. and Floudas, C. A. }, citeulike-article-id = {2931886}, doi = {http://dx.doi.org/10.1002/prot.10521}, issn = {1097-0134}, journal = {Proteins}, keywords = {energy, protein, scp, structure}, month = {February}, number = {2}, pages = {303--314}, posted-at = {2008-06-26 18:57:20}, priority = {2}, title = {A new pairwise folding potential based on improved decoy generation and side-chain packing.}, url = {http://dx.doi.org/10.1002/prot.10521}, volume = {54}, year = {2004} }

TY - JOUR ID - citeulike:2931886 L3 - citeulike-article-id:2931886 TI - A new pairwise folding potential based on improved decoy generation and side-chain packing. JF - Proteins VL - 54 IS - 2 SP - 303 EP - 314 AD - Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08540, USA. SN - 1097-0134 N2 - A new force field for pairwise residue interactions as a function of C(alpha) to C(alpha) distances is presented. The force field was developed through the solution of a linear programming formulation with large sets of constraints. The constraints are based on the construction of >80,000 low-energy decoys for a set of proteins and requiring the decoy energies for each protein system to be higher than the native conformation of that particular protein. The generation of a robust force field was facilitated by the use of a novel decoy generation process, which involved the rational selection of proteins to add to the training set and included a significant energy minimization of the decoys. The force field was tested on a large set of decoys for various proteins not included in the training set and shown to perform well compared with a leading force field in identifying the native conformation for these proteins. KW - energy KW - protein KW - scp KW - structure AU - Loose, C AU - Klepeis, JL AU - Floudas, CA PY - 2004/02/01/ UR - http://dx.doi.org/10.1002/prot.10521 ER -