期刊
CHEMICAL PHYSICS LETTERS
卷 559, 期 -, 页码 94-98出版社
ELSEVIER
DOI: 10.1016/j.cplett.2012.12.063
关键词
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资金
- Strategic Programs for Innovative Research (SPIRE) of the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan
- Computational Materials Science Initiative (CMSI), Japan
- Japan Society for the Promotion of Science (JSPS)
- MEXT
- Grants-in-Aid for Scientific Research [23651202, 23370066, 21300111, 20118001, 23370068, 20118002] Funding Source: KAKEN
We propose a method for calculating the binding free energy of protein-ligand complexes using all-atom molecular dynamics simulation combined with the solution theory in the energy representation. Four distinct modes for the binding of tri-N-acetyl-D-glucosamine (triNAG) to hen egg-white lysozyme were investigated, one from the crystal structure and three generated by docking predictions. The proposed method was demonstrated to be used to distinguish the most plausible binding mode (crystal model) as the lowest binding energy mode. (c) 2013 Elsevier B.V. All rights reserved.
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