NAMD SCALABLE MOLECULAR DYNAMICS SOFTWARE

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DESCRIPTION (provided by applicant): The Resource for Macromolecular Modeling and Bioinformatics seeks to bring the most advanced molecular modeling, bioinformatic, and computational technologies to bear on questions of biomedical interest. We will extend and refine these technologies in response to experimental advances. We will multiply the impact of our work through direct collaboration with experimental researchers, by the distribution of high quality and easily adopted software, and with a comprehensive training, service, and dissemination effort.The Resource has assembled a multidisciplinary team that has focused on the modeling of large macromolecular systems in realistic environments, and produced insights into biomolecular processes coupled to mechanical force, bioelectronic processes in metabolism and vision, and the function and mechanism of membrane proteins.In the next funding period, the Resource will pursue six specific aims: * Develop molecular modeling tools which can integrate structural information with bioinformaticsdatabases and molecular dynamics simulations, and which can be used by a wide audience; * Provide high performance molecular visualization and simulation software, capable ofmodeling biomolecules in realistic environments of 100,000 atoms or more; * Advance the conceptual and methodological foundations of molecular modeling in the fields of quantum biology, mechanobiology, and interactive modeling; * Advance biomedical science through collaborations between theoretical and experimental researchers; * Support the entire research process through a web-enabled collaborative environment; * Ehance service, training, and dissemination by leveraging web-based molecular graphics and integrated modeling technologies.