title: Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes.
abstract: 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-protein 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.
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan.|Genomics Research Institute, Academia Sinica , Taipei 115, Taiwan.
authors.forename: Jon D
authors.initials: JD
authors.lastname: Wright
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan.
authors.forename: Karen
authors.initials: K
authors.lastname: Sargsyan
authors.affiliation: Laboratory of Computational Biology, NHLBI, National Institutes of Health , Bethesda, Maryland, United States.
authors.forename: Xiongwu
authors.initials: X
authors.lastname: Wu
authors.affiliation: Laboratory of Computational Biology, NHLBI, National Institutes of Health , Bethesda, Maryland, United States.
authors.forename: Bernard R
authors.initials: BR
authors.lastname: Brooks
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica , Taipei 115, Taiwan.|Department of Chemistry, National Tsinghua University , Hsinchu 300, Taiwan.
authors.forename: Carmay
authors.initials: C
authors.lastname: Lim