Jang Yunho, Jeong Jay I, Kim Moon K
Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003, USA.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W57-62. doi: 10.1093/nar/gkl039.
UMass Morph Server (UMMS) has been developed for the broad impact on the study of molecular dynamics (MD). The elastic network model (ENM) of a given macromolecule has been proven as a useful tool for analyzing thermal behaviors locally and predicting folding pathways globally. UMMS utilizes coarse-grained ENMs at various levels. These simplifications remarkably save computation time compared with all-atom MD simulations so that one can bring down massive computational problems from a supercomputer to a PC. To improve computational efficiency and physical reality of ENMs, the symmetry-constrained, rigid-cluster, hybrid and chemical-bond ENMs have been developed and implemented at UMMS. One can request both harmonic normal mode analysis of a single macromolecule and anharmonic pathway generation between two conformations of a same molecule using elastic network interpolation at http://biomechanics.ecs.umass.edu/umms.html.
马萨诸塞大学形态服务器（UMMS）的开发是为了对分子动力学（MD）研究产生广泛影响。给定大分子的弹性网络模型（ENM）已被证明是一种用于局部分析热行为和全局预测折叠途径的有用工具。UMMS在不同层次上使用粗粒度的ENM。与全原子MD模拟相比，这些简化显著节省了计算时间，从而使人们能够将大量计算问题从超级计算机转移到个人电脑上。为了提高ENM的计算效率和物理真实性，对称约束、刚性簇、混合和化学键ENM已在UMMS上开发并实现。人们可以通过http://biomechanics.ecs.umass.edu/umms.html使用弹性网络插值请求对单个大分子进行简正模式分析以及生成同一分子两个构象之间的非简正途径。
