New Tutorial: Basics of membrane-protein interactions using molecular dynamics with NAMD, VMD, and CHARMM-GUI
This new tutorial is designed to introduce preparation, modeling, and analysis of membrane-protein system with molecular dynamics (MD) using NAMD, VMD, and CHARMM-GUI. The system of interest is the outer membrane phospholipase A from E. coli (OmpLA, PDB ID 1QD5, Snijder HJ, …, Dijkstra BW, Nature, 401, 717, 1999). In a recent experimental study the Fleming Lab (Johns Hopkins) used spontaneous folding of OmpLA into the membrane to prepare a hydrophobicity scale (Moon PC and Fleming KG, PNAS 108, 10174, 2011)
No prior knowledge of molecular dynamics software packages is required.
The tutorial is available via the following link: Basics of membrane-protein interactions using molecular dynamics with NAMD, VMD, and CHARMM-GUI
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