Abstract
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.
Keywords: Quantum chemistry, fragment molecular orbital, drug design, ab initio, GAMESS, FMO, QM/MM, FBDD, SBDD.
Current Topics in Medicinal Chemistry
Title:GAMESS As a Free Quantum-Mechanical Platform for Drug Research
Volume: 12 Issue: 18
Author(s): Yuri Alexeev, Michael P. Mazanetz, Osamu Ichihara and Dmitri G. Fedorov
Affiliation:
Keywords: Quantum chemistry, fragment molecular orbital, drug design, ab initio, GAMESS, FMO, QM/MM, FBDD, SBDD.
Abstract: 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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Alexeev Yuri, P. Mazanetz Michael, Ichihara Osamu and G. Fedorov Dmitri, GAMESS As a Free Quantum-Mechanical Platform for Drug Research, Current Topics in Medicinal Chemistry 2012; 12 (18) . https://dx.doi.org/10.2174/1568026611212180008
DOI https://dx.doi.org/10.2174/1568026611212180008 |
Print ISSN 1568-0266 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4294 |
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