Loose C, Klepeis J L, Floudas C A
Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08540, USA.
Proteins. 2004 Feb 1;54(2):303-14. doi: 10.1002/prot.10521.
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.
提出了一种新的成对残基相互作用的力场，它是Cα到Cα距离的函数。该力场是通过求解具有大量约束条件的线性规划公式而开发的。这些约束条件基于为一组蛋白质构建超过80,000个低能诱饵，并要求每个蛋白质系统的诱饵能量高于该特定蛋白质的天然构象。通过使用一种新颖的诱饵生成过程，促进了稳健力场的生成，该过程涉及合理选择要添加到训练集中的蛋白质，并包括对诱饵进行显著的能量最小化。该力场在一大组未包含在训练集中的各种蛋白质的诱饵上进行了测试，结果表明，与领先的力场相比，它在识别这些蛋白质的天然构象方面表现良好。
