Protein鈥揚rotein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes

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• 作者：Jon D. Wright ; Karen Sargsyan ; Xiongwu Wu ; Bernard R. Brooks ; Carmay Lim
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2013
• 出版时间：September 10, 2013
• 年：2013
• 卷：9
• 期：9
• 页码：4186-4194
• 全文大小：321K
• 年卷期：v.9,no.9(September 10, 2013)
• ISSN：1549-9626

文摘

In this work, we have (i) evaluated the ability of the EMAP method implemented in the CHARMM program to generate the correct conformation of Ab/Ag complex structures and (ii) developed a support vector machine (SVM) classifier to detect native conformations among the thousands of refined Ab/Ag configurations using the individual components of the binding free energy based on a thermodynamic cycle as input features in training the SVM. Tests on 24 Ab/Ag complexes from the protein鈥損rotein docking benchmark version 3.0 showed that based on CAPRI evaluation criteria, EMAP could generate medium-quality native conformations in each case. Furthermore, the SVM classifier could rank medium/high-quality native conformations mostly in the top six among the thousands of refined Ab/Ag configurations. Thus, Ab-Ag docking can be performed using different levels of protein representations, from grid-based (EMAP) to polar hydrogen (united-atom) to all-atom representation within the same program. The scripts used and the trained SVM are available at the www.charmm.org forum script repository.