Journal
CURRENT TOPICS IN MEDICINAL CHEMISTRY
Volume 12, Issue 18, Pages 2013-2033Publisher
BENTHAM SCIENCE PUBL LTD
DOI: 10.2174/156802612804910269
Keywords
Quantum chemistry; fragment molecular orbital; drug design; ab initio; GAMESS; FMO; QM/MM; FBDD; SBDD
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Funding
- Office of Science of the U.S. Department of Energy [DE-AC02-06CH11357]
- Next Generation Super Computing Project, Nanoscience Program (MEXT, Japan)
- Strategic Programs for Innovative Research (SPIRE, Japan)
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Driven by a steady improvement of computational hardware and significant progress in ab initio method development, quantum-mechanical approaches can now be applied to large biochemical systems and drug design. We review the methods implemented in GAMESS, which are suitable to calculate large biochemical systems. An emphasis is put on the fragment molecular orbital method (FMO) and quantum mechanics interfaced with molecular mechanics (QM/MM). The use of FMO in the protein-ligand binding, structure-activity relationship (SAR) studies, fragment-and structure-based drug design (FBDD/SBDD) is discussed in detail.
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