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Center for Macromolecular Modeling and Bioinformatics

Klaus J. Schulten, Ph.D.
P41RR005969
Active

Center Overview

The Center for Macromolecular Modeling and Bioinformatics brings the most advanced molecular modeling and simulation, bioinformatics, and computational technologies to bear on questions of biomedical relevance. It extends, refines and delivers these technologies in response to experimental progress and emerging needs of the wide biomedical research community. The impact of the work is magnified through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. Specifically, the Center develops and disseminates molecular modeling, simulation, and visualization technologies and software that are used to study a wide range of molecular phenomena in biology and medicine. The Center's sizeable multidisciplinary team is engaged in the modeling of large macromolecular systems in realistic environments, and has produced ground-breaking insights into biomolecular processes coupled with mechanical force, bioelectronic processes in metabolism and vision, and the mechanism of membrane proteins. The Center is committed to further advancement of molecular modeling and simulation tools used by a wide audience, high performance molecular visualization and simulation software capable of modeling biomolecules in realistic environments of 100,000,000 atoms or larger, conceptual and methodological foundations of molecular modeling, and biomedical science through collaborations with theoretical and experimental researchers. Major software tools include the highly scalable molecular simulation program NAMD (Nanoscale Molecular Dynamics), and the advanced molecular visualization program VMD (Visual Molecular Dynamics).

Impact on Human Health

All areas of modern biology and medicine have been increasingly relying on developing a deeper understanding of the underlying molecular phenomena of human health and disease. The molecular modeling and simulation tools developed by the Center are key components for molecular research in various areas of biomedical sciences. Complementing the fast progress made in experimental structural biology of such phenomena, computational modeling and visualization technologies provided by the Center are used to study structure-function relationship of a wide range of biomedically relevant molecular systems, such as receptors, membrane channels and transporters, structural and metabolic proteins, as well as viral and bacterial proteins that are involved in pathogenesis of infection diseases. Such studies not only provide the much needed molecular framework for characterizing the underlying mechanism of human health and diseases, but also expand the scope of rational drug design through offering novel targets for pharmacological intervention.

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
NAMD
Center for Macromolecular Modeling and Bioinformatics
NIGMS

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations.

Linux, Mac OSX, Windows AMBER, AMBER 'binpos' trajectory...(more) N/A N/A
VMD
Center for Macromolecular Modeling and Bioinformatics
NIGMS

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.  VMD incorporates built-in tools for structure building, simulation analysis, sequence alignment, photorealistic ray tracing, and movie making.  VMD supports multi-core CPUs, parallel computers, and it benefits from GPU-accelerated computing for demanding analysis and visualization computations.

Linux, Mac OSX, Windows AMBER, AMBER "CRD" trajectory...(more) N/A N/A