Journal
CHEMICAL PHYSICS LETTERS
Volume 535, Issue -, Pages 157-162Publisher
ELSEVIER
DOI: 10.1016/j.cplett.2012.03.046
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Funding
- RISS at the Institute of Industrial Science (IIS) of the University of Tokyo
- SFR by Rikkyo University
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The reliability of protein structure is a critical concern to grasp the insights with respect to residue-residue and residue-ligand interactions by computational methods. In such calculations, the molecular geometries are usually prepared by the optimization of experimental structure with empirical molecular mechanics (MM) parameters. As an alternative to MM methods, we have developed a partial geometry optimization with the fragment molecular orbital (FMO) scheme at the second-order Moller-Plesset perturbation (MP2) level. The TrpCage miniprotein was used as a demonstrative example. The geometries of the central region were partially optimized at the FMO-MP2 and Hartree-Fock (FMO-HF) levels, and the former with the correlation correction showed reasonable agreement with the experimental structure. (C) 2012 Elsevier B.V. All rights reserved.
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