| Protein-ligand binding free energy calculation by the Smooth Reaction Path Generation (SRPG) Method. | |
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MedLine Citation:
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PMID: 19807195 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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We developed a new molecular dynamics simulation method for protein-ligand binding free energy calculation in an explicit water model. This method consists of three steps: (1) generation of a compound dissociation path starting from a stable protein-compound complex structure, (2) calculation of the free energy surface along the dissociation path, and (3) calculation of the free energy surface of a small area around the protein-compound complex structure, which is a free energy minimum. The protein-compound binding free energy is estimated from the information obtained by the above three steps. This method was applied to a small system, a 18-crown-6 ether with its ligand ion, and a realistic system consisting of a target protein with its inhibitor. This approximation worked well; the protein-inhibitor dissociation was successfully performed, and the binding free energies were calculated. |
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Authors:
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Yoshifumi Fukunishi; Daisuke Mitomo; Haruki Nakamura |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Journal of chemical information and modeling Volume: 49 ISSN: 1549-9596 ISO Abbreviation: - Publication Date: 2009 Aug |
Date Detail:
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Created Date: 2009-10-07 Completed Date: 2009-10-22 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 101230060 Medline TA: J Chem Inf Model Country: United States |
Other Details:
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Languages: eng Pagination: 1944-51 Citation Subset: IM |
Affiliation:
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Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan. y-fukunishi@aist.go.jp |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Biotin
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chemistry,
metabolism Computer Simulation Crown Ethers / chemistry Ligands Models, Molecular Molecular Conformation Protein Binding Proteins / antagonists & inhibitors, chemistry*, metabolism Streptavidin / antagonists & inhibitors, chemistry, metabolism Thermodynamics* |
| Chemical | |
Reg. No./Substance:
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0/Crown Ethers; 0/Ligands; 0/Proteins; 58-85-5/Biotin; 9013-20-1/Streptavidin |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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