Moltemplate a Coarse-Grained Model Assembly Tool

View Large Image | View Hi-Res Image | Download PowerPoint SlideMoltemplate, an open-source program intended for building large scale coarse-grained models, has been developed by our group to facilitate the speed and ease by which such models could be constructed. Although coarse-grained models have long been considered as an indispensable tool in the investigation of biopolymer dynamics and assembly, the actual process of constructing such models is often arduous and impeded by the fact that complex and unconventional force fields must be implemented. Until now, no software has existed for building general coarse-grained biomolecules, and as a result, the use of such models remained relatively inaccessible. Here, we represent a general molecule-builder program, Moltemplate, which together with the LAMMPS simulation program, will hopefully bridge the current gap and bring coarse-grained simulations to a wider audience. As an demonstration of its functionality, we would like to represent its use in the investigation of the nucleation of amyloid fibrils. We have found that context-induced effects (such as alternative folding of the monomer) can have profound consequences on the assembled product (such as the morphology, growth-potential and stability of the aggregate). Other examples, such the stability of membrane proteins, and the growth of microtubules will be discussed.