Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.
Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.
Wang
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Graduate Group in Biophysics, University of California San Francisco, California 94143, USA. wwang@cgl.ucsf.edu
Donini
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Reyes
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Kollman
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D002384:Catalysis; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D008024:Ligands; D008956:Models, Chemical; D015233:Models, Statistical; D009696:Nucleic Acids / Q000378:metabolism; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D013816:Thermodynamics
D004798:Enzymes; D008024:Ligands; D009696:Nucleic Acids; D011506:Proteins