Department of Biophysics, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan.
Department of Physics, Nanjing University , Nanjing 210093, China.
J Chem Theory Comput. 2011 Jun 14;7(6):1979-89. doi: 10.1021/ct2001045. Epub 2011 May 19.
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 .
为了在毫秒时间尺度或更长时间内模拟蛋白质的工作，我们开发了一种粗粒度（CG）分子动力学（MD）方法和软件，即 CafeMol。在一个残基一个粒子的分辨率下，CafeMol 配备了四种基于结构的蛋白质模型：（1）无格子 Go 模型，（2）用于天然状态和折叠动力学的基于原子相互作用的 CG 模型，（3）用于构象变化动力学的多势阱模型，以及（4）用于天然结构周围准谐波动的弹性网络模型。配体可以被明确或隐含地处理。为了模拟由外部力驱动的蛋白质的功能运动，CafeMol 具有各种灵活的方法来“切换”诱导蛋白质主动运动的能量函数。CafeMol 可以使用中等大小的 PC 集群进行并行计算。我们描述了 CafeMol 方法，并通过几个例子来说明，如 F1-ATP 酶的旋转运动和转运体中药物的输出。CafeMol 的源代码可在 www.cafemol.org 获得。
