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Molecular dynamics
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Molecular dynamics is the study of the movement of molecules. This could be tracing how a molecule or a collection of molecules moves trough space ie. in a gas or a solvent, or it could be conformational change. The first case is usually for simulating thermodynamic properties whereas the later is usefull for studying molecules of biological interest. This could be protein folding or binding of drug a molecule to its protein or DNA target.
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In this example the undecapeptide substance P (NMR solution structure 1 of entry 1N6T in PDB) was subjected to 1000 ps. of stocastic dynamics. Snapshots was taken at various time intervals. The initial structure is an alpha helix which gradially unvinds.
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Molecular Mechanics (MM)
Pharmacophore Modeling
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Molecular Quantum Mechanics
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