A new pairwise folding potential based on improved decoy generation and side-chain packing |
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Authors: | Loose C Klepeis J L Floudas C A |
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Affiliation: | Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08540, USA. |
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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. |
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Keywords: | energy model linear optimization protein decoys threading structure prediction protein design force field potential model |
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