Applications

A variety of (bio)molecular systems of practical interest is simulated to obtain a microscopic picture of their structure and dynamics, e.g. inhibitor binding to plasmepsin II, structure of lipid bilayers or micelles, the stability of polypeptides in different solvents, etc.

MD Simulation has been applied to a variety of biomolecular systems with the aim of understanding biomolecular phenomena or processes, or in order to help interpret experimental observations. Here we only mention as examples a few recent applications in different areas of research.

MD simulation of conformational ensembles may help to interpret X-ray, CD or NMR data, see e.g. [99.15, 02.40, 03.21, 04.35, 05.42, 06.38, 07.09, 08.02, 09.07, 09.09, 09.17, 09.23, 10.05, 10.14, 10.41, 12.01, 12.14, 12.15, 13.02, 13.11, 13.19, 13.21, 14.03, 14.12]
Antibody, polysaccharide, and protein stability has been studied as function of solute or solvent composition [00.17, 04.25, 05.03, 07.11, 07.14, 07.31, 08.01, 08.02, 08.09, 08.19, 08.20, 09.10, 09.16, 10.01, 10.03, 10.13, 10.15, 10.37, 10.44, 12.22, 13.04, 13.16,13.17,14.01]
Reversible polypeptide folding under different thermodynamic conditions and solute/solute composition has been extensively studied [02.40, 04.35, 01.01, 01.10, 02.42, 04.01, 04.30, 04.32, 04.34, 04.36, 05.33, 05.42, 06.01, 06.04, 06.08, 07.05, 07.24, 08.03, 08.06, 09.08, 09.12, 10.09, 10.11, 10.40, 11.01, 11.14, 11.28, 12.18, 13.15]
Ligand-binding free energies and conformational preferences have been calculated for various proteins [03.17, 04.03, 05.22, 05.04, 05.15, 07.04, 07.09, 08.17, 10.17, 10.43, 11.12, 11.24, 12.12]
An enzyme and chemical reactions have been analyzed using simulation [01.07, 07.28, 10.12, 12.03, 12.29, 13.12]
Membrane simulations are carried out to study stability, pore formation, transport, peptide binding, etc. [04.27, 05.26, 05.34, 06.03, 06.18, 10.38]

The references to publications are coded according to the IGC DownloadMD publication list (PDF, 888 KB).