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Application of the fuzzy‐oil‐drop model to membrane protein simulation
Author(s) -
Zobnina Veronica,
Roterman Irena
Publication year - 2009
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22443
Subject(s) - membrane , molecular dynamics , membrane protein , biological system , molecule , drop (telecommunication) , computer simulation , chemistry , materials science , computer science , simulation , engineering , mechanical engineering , biochemistry , computational chemistry , biology , organic chemistry
Abstract 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. Proteins 2009. © 2009 Wiley‐Liss, Inc.