Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation 英文参考文献.docVIP

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Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation 英文参考文献.doc

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Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation 英文参考文献

Pharmaceuticals 2012, 5, 1064-1079; doi:10.3390/ph5101064 OPEN ACCESS pharmaceuticals ISSN 1424-8247 /journal/pharmaceuticals Article Statistical Estimation of the Protein-Ligand Binding Free Energy Based On Direct Protein-Ligand Interaction Obtained by Molecular Dynamics Simulation Yoshifumi Fukunishi 1,* and Haruki Nakamura 2 1 Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan 2 Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mail: harukin@protein.osaka-u.ac.jp * Author to whom correspondence should be addressed; E-Mail: y-fukunishi@aist.go.jp; Tel.: +81-3-3599-8290; Fax: +81-3-3599-8099. Received: 29 August 2012; in revised form: 19 September 2012 / Accepted: 21 September 2012 / Published: 28 September 2012 Abstract: We have developed a method for estimating protein-ligand binding free energy (?G) based on the direct protein-ligand interaction obtained by a molecular dynamics simulation. Using this method, we estimated the ?G value statistically by the average values of the van der Waals and electrostatic interactions between each amino acid of the target protein and the ligand molecule. In addition, we introduced fluctuations in the accessible surface area (ASA) and dihedral angles of the protein-ligand complex system as the entropy terms of the ?G estimation. The present method included the fluctuation term of structural change of the protein and the effective dielectric constant. We applied this method to 34 protein-ligand complex structures. As a result, the correlation coefficient between the experimental and calculated ?G values was 0.81, and the average error of ?G was 1.2 kcal/mol with the use of the fixed parameters. These results were obtained from a 2 nsec molecular dynamics simulation. Keywords: protein-ligand docking; mol