AMBER/PBSA: An Open-Source Computer Program for Accurate and Scalable Solvation Analysis of Biomolecules

University Of California-Irvine, Irvine CA

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Abstract

? DESCRIPTION (provided by applicant): Atomistic simulations of biomolecules provide a detailed view of structure and dynamics that complement experiments. Increased conformational sampling, enabled by new algorithms and growth in computer power, now allows a much broader range of events to be observed, providing critical insights, largely inaccessible to experiments. Advancements in implicit solvation treatments have furthered the simulation reach to a broader range of studies of biomolecular structure, dynamics and function, including protein folding and misfolding, protein structure prediction, protein-ligand binding, enzyme mechanisms, and drug design. The AMBER/PBSA program is an open-source computer program for implicit solvation modeling of biomolecules. In this project, we propose to continue the maintenance and improvement of the AMBER/PBSA program by (1) growing and improving the AMBER/PBSA program in response to suggestions by our users; (2) developing and integrating lightweight analysis tools to facilitate better molecular simulations; (3) developing dielectric model for complex systems without apparent solvent/solute interface; and (4) continuing to validate the PB models.