title: UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models.
abstract: 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.
authors.affiliation: Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, MA 01003, USA.
authors.forename: Yunho
authors.initials: Y
authors.lastname: Jang
authors.forename: Jay I
authors.initials: JI
authors.lastname: Jeong
authors.forename: Moon K
authors.initials: MK
authors.lastname: Kim
mesh_terms: D019295:Computational Biology; D004548:Elasticity; D020407:Internet; D046911:Macromolecular Substances / Q000737:chemistry*; D008958:Models, Molecular; D009038:Motion; D012984:Software
chemical_list: D046911:Macromolecular Substances