New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein StructuresClick to copy article linkArticle link copied!
- Xinxiang WangXinxiang WangSchool of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. ChinaMore by Xinxiang Wang
- Di ZhangDi ZhangSchool of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. ChinaMore by Di Zhang
- Sheng-You Huang*Sheng-You Huang*E-mail: [email protected]. Phone: +86-27-87543881. Fax: +86-027-87556576.School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. ChinaMore by Sheng-You Huang
Abstract
Accurate prediction of a protein’s structure requires a reliable free energy function that consists of both enthalpic and entropic contributions. Although considerable progresses have been made in the calculation of potential energies in protein structure prediction, the computation for entropies of protein has lagged far behind, due to the challenge that estimation of entropies often requires expensive conformational sampling. In this study, we have used a knowledge-based approach to estimate the backbone conformational entropies from experimentally determined structures. Instead of conducting computationally expensive MD/MC simulations, we obtained the entropies of protein structures based on the normalized probability distributions of back dihedral angles observed in the native structures. Our new knowledge-based scoring function with inclusion of the backbone entropies, which is referred to as ITScoreDA or ITDA, was extensively evaluated on 16 commonly used decoy sets and compared with 50 other published scoring functions. It was shown that ITDA is significantly superior to the other tested scoring functions in selecting native structures from decoys. The present study suggests the role of backbone conformational entropies in protein structures and provides a way for fast estimation of the entropic effect.
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