title: CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work.
abstract: For simulating proteins at work in millisecond time scale or longer, we develop a coarse-grained (CG) molecular dynamics (MD) method and software, CafeMol. At the resolution of one-particle-per-residue, CafeMol equips four structure-based protein models: (1) the off-lattice Go model, (2) the atomic interaction based CG model for native state and folding dynamics, (3) the multiple-basin model for conformational change dynamics, and (4) the elastic network model for quasiharmonic fluctuations around the native structure. Ligands can be treated either explicitly or implicitly. For mimicking functional motions of proteins driven by some external force, CafeMol has various and flexible means to "switch" the energy functions that induce active motions of the proteins. CafeMol can do parallel computation with modest sized PC clusters. We describe CafeMol methods and illustrate it with several examples, such as rotary motions of F1-ATPase and drug exports from a transporter. The CafeMol source code is available at www.cafemol.org .
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Hiroo
authors.initials: H
authors.lastname: Kenzaki
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Nobuyasu
authors.initials: N
authors.lastname: Koga
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Naoto
authors.initials: N
authors.lastname: Hori
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Kanada
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan.|Department of Physics, Nanjing University , Nanjing 210093, China.
authors.forename: Wenfei
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Physics, School of Advanced Science and Engineering, Waseda University , Tokyo 169-8555, Japan.
authors.forename: Kei-Ichi
authors.initials: K
authors.lastname: Okazaki
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan.
authors.forename: Xin-Qiu
authors.initials: XQ
authors.lastname: Yao
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan.|Advanced Center for Computing and Communication, RIKEN , Wako Saitama 351-0198, Japan.
authors.forename: Shoji
authors.initials: S
authors.lastname: Takada