The long-term objective of this project is to develop an efficient simulation method that permits studies of biomolecular interactions involving molecular sizes and time scales that are not possible with the current state of the art methods that use atom-based potentials. The major theme of our proposal is to extend currently available residue-based potentials to provide better anisotrophic behavior while maintaining the significantly reduced amount of computations compared to an equivalent atomistic model. The development and adaptation of these next generation residue-based potentials to molecular dynamics will result in unmatched accuracy and speed. We believe that this new simulation capability will be a significant step towards understanding many pathogenic and non-pathogenic biological processes on unprecedented scales: the formation of protein assemblies, dynamics of protein-DNA complexes, muscle concentration, signal transduction processes, the exact role of chaperons in protein folding, and protein-membrane interactions.
Our technology will aid pharmaceutical and biotechnology companies in developing new strategies against pathogenic processes that involve large proteins or protein assemblies. We will commercialize this technology through software licensing and contract services. The software product will be an add-on module for CHARMM and/or MBO(N)D.
