Potential of mean force for protein-protein interaction studies | |
Jiang, L ; Gao, Y ; Mao, FL ; Liu, ZJ ; Lai, LH | |
刊名 | proteins structure function and genetics
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2002 | |
关键词 | pair potentials knowledge-based potentials protein association protein-protein interaction protein recognition FREE-ENERGY CALCULATIONS LIGAND INTERACTIONS CRYSTAL-STRUCTURE 3-DIMENSIONAL STRUCTURE SCORING FUNCTION HYDROGEN-BONDS BINDING COMPLEXES INHIBITOR SPECIFICITY |
DOI | 10.1002/prot.10031 |
英文摘要 | Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology. We calculate atom pair potentials for 16 pair interactions, which can reflect the importance of hydrophobic interactions and specific hydrogen-bonding interactions. The derived potentials for hydrogen-bonding interactions show a valley of favorable interactions at a distance of approximate to3 Angstrom, corresponding to that of an established hydrogen bond. For the test set of 28 protein complexes, the calculated energies have a correlation coefficient of 0.75 compared with experimental binding free energies. The performance of the method in ranking the binding energies of different protein-protein complexes shows that the energy estimation can be applied to value binding free energies for protein-protein associations. Proteins 2002;46:190-196. (C) 2001 Wiley-Liss, Inc.; Biochemistry & Molecular Biology; Biophysics; SCI(E); 50; 2; 190-196; 46 |
语种 | 英语 |
内容类型 | 期刊论文 |
源URL | [http://ir.pku.edu.cn/handle/20.500.11897/210795] ![]() |
专题 | 化学与分子工程学院 |
推荐引用方式 GB/T 7714 | Jiang, L,Gao, Y,Mao, FL,et al. Potential of mean force for protein-protein interaction studies[J]. proteins structure function and genetics,2002. |
APA | Jiang, L,Gao, Y,Mao, FL,Liu, ZJ,&Lai, LH.(2002).Potential of mean force for protein-protein interaction studies.proteins structure function and genetics. |
MLA | Jiang, L,et al."Potential of mean force for protein-protein interaction studies".proteins structure function and genetics (2002). |
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