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GAMESS as a free quantum-mechanical platform for drug research
Yuri Alexeev1, Michael P Mazanetz, Osamu Ichihara
1Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Building 240, Argonne, IL 60439, USA.
Current Topics in Medicinal Chemistry
|November 1, 2012
Summary
Quantum mechanical methods, including fragment molecular orbital (FMO) and QM/MM, are now applicable to large biochemical systems for drug design. These computational approaches aid in understanding protein-ligand binding and structure-activity relationships.
Area of Science:
- Computational Chemistry
- Biochemistry
- Drug Discovery
Background:
- Advancements in computational hardware and ab initio methods enable quantum-mechanical (QM) calculations for large systems.
- QM approaches are increasingly vital in modern drug design and biochemical research.
Purpose of the Study:
- To review QM methods in the GAMESS software suitable for large biochemical systems.
- To highlight the application of fragment molecular orbital (FMO) and QM/MM methods.
- To discuss the utility of FMO in drug design contexts.
Main Methods:
- Review of QM methods available in GAMESS.
- Focus on fragment molecular orbital (FMO) method.
- Focus on quantum mechanics interfaced with molecular mechanics (QM/MM).
Main Results:
- GAMESS provides methods applicable to large biochemical systems.
- FMO and QM/MM are key QM approaches for these systems.
- Detailed discussion on FMO applications in drug design.
Conclusions:
- Modern computational chemistry tools like GAMESS facilitate large-scale QM calculations.
- FMO and QM/MM methods are powerful for studying protein-ligand interactions and SAR.
- These methods significantly advance fragment- and structure-based drug design.
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