Computational Modeling Core

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All efforts within the Membrane Protein Structural Dynamics Consortium (MPSDC) are aimed at gaining a deep mechanistic understanding of membrane protein function, linking structure to dynamics. The Computational Modeling Core D4, referred to as CMC, is a central unifying component of the MPSDC, serving as the “glue” to assemble experimental data into a coherent physical picture. The goals of the CMC are to provide an intellectual resource to develop, validate and apply novel methods and technologies that support and integrate with the specific experimental studies in the MPSDC, as well as to facilitate the integration and dissemination of these computational methods within the MPSDC and the scientific community at large. Emphasis is placed on computational approaches that can enhance and deepen mechanistic insight by enabling valid and quantitative comparisons with experimental data. The research plan of the CMC is organized around three Specific Aims: Multi-Resolution Structural Modeling (Aim 1), where we develop an integrated multi- resolution computational framework to leverage the information that can be harvested from a diverse range of complementary experimental techniques to discover and/or to refine structural models of the different functional forms/states accessible to membrane proteins; Force Fields and Physical Representation of Membrane Proteins (Aim 2), where we will broaden the scope of open-access web- based tools to carry out state-of-the-art computations and establish standardized computational protocols to achieve the most realistic and accurate physical representation of membrane protein systems; and Conformational Transition Pathways and Functional Motions (Aim 2) where we advance the simulation tools for the determination of conformational transition pathways in large membrane proteins, and provide means to design experiments to test and validate those computational pathways.