Application of the fuzzy-oil-drop model to membrane protein simulation.
The analysis of structural properties and biological activity of membrane proteins requires long lasting simulation of molecular dynamics. The large number of atoms present in protein molecule, membrane (phospholipids), and water environment makes the simulation of large scale. The implementation of simplified model representing the natural environment for membrane proteins is presented and compared with the vacuum simulation and simulation in the presence of water molecules and membrane phospholipids presented explicite. The comparative structural analysis and computational times for these three models makes the simplified model promising.
Zobnina
Veronica
V
Department of Bioinformatics and Telemedicine, Collegium Medicum-Jagiellonian University, Krakow, Poland.
Roterman
Irena
I
D000818:Animals; D002417:Cattle; D019295:Computational Biology; D003198:Computer Simulation; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D055355:Opsins / Q000737:chemistry*; D012243:Rhodopsin / Q000737:chemistry*; D012984:Software; D013816:Thermodynamics
D008565:Membrane Proteins; D055355:Opsins; D012243:Rhodopsin