title: A new pairwise folding potential based on improved decoy generation and side-chain packing.
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.
authors.affiliation: Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08540, USA.
authors.forename: C
authors.initials: C
authors.lastname: Loose
authors.forename: J L
authors.initials: JL
authors.lastname: Klepeis
authors.forename: C A
authors.initials: CA
authors.lastname: Floudas
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D013816:Thermodynamics
chemical_list: D011506:Proteins