Supervised Molecular Dynamics (SuMD) Approaches in Drug Design
Supervised MD (SuMD) is a computational method that enables the exploration of ligand–receptor recognition pathway in a reduced timescale. The performance speedup is due to the incorporation of a tabu-like supervision algorithm on the ligand–receptor approaching distance into a classic molecular dynamics (MD) simulation. SuMD enables the investigation of ligand–receptor binding events independently from the starting position, chemical structure of the ligand (small molecules or peptides), and also from its receptor-binding affinity. The application of SuMD highlights an appreciable capability of the technique to reproduce the crystallographic structures of several ligand–protein complexes and can provide high-quality protein–ligand models of for which yet experimental confirmation of binding mode is not available.
Key wordsLigand–protein binding Peptide–protein binding Recognition pathway Molecular dynamics Supervised molecular dynamics Meta-binding site
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