The Center for Macromolecular Modeling and Bioinformatics develops software tools to model cellular processes in atomic detail. An experienced, multidisciplinary team of researchers at the Center provides for the biomedical research community a """"""""computational microscope"""""""" equipped with molecular visualization, sequence, structure and dynamics analysis, and collaborates with leading experimental laboratories. The Center will expand the use of its computational tools to a broad range of biomedical research problems and provide easy access to these tools for the biomedical research community. In the next funding period, the Center will pursue the following specific aims: ?Raise performance, efficiency, and accuracy of simulations for cellular processes. Facilitate innovation in the biomedical research community by providing accessible simulation tools supporting, in particular, enhanced sampling, coarse-grained models, and quantum effects; ?Support visualization and analysis of biomolecular systems with powerful, customizable software packages, integrating multi-modal structure viewing and analysis with model building and simulation tools; ?Enhance performance for visualization, analysis, and modeling of large size and long timescale cellular processes by exploiting emerging technologies such as graphics processor accelerators and solid state disks; ?Develop methods to model large cellular domains such as membrane environments;improve tools for structure prediction and refinement, e.g., for large, flexible protein-RNA assemblies. Scale coarse-grained simulation methods to eukaryotic-sized cells; ?Drive the development of novel computational tools and methods through collaborations with both theoretical and experimental laboratories; ?Enhance service, training, and dissemination, providing a cutting edge computational laboratory, hands-on training, first-rate educational material, and an extensive, widely-used website to biomedical researchers.
The Center for Macromolecular Modeling and Bioinformatics pioneers computer-based biomedical research into cellular processes and nanoengineering. The Center makes emerging technologies available to the biomedical research community, develops powerful simulation tools for biomolecular processes related to health and disease, and provides these tools to the greater biomedical community for the purpose of developing new diagnostic tools and drug treatments.
|Gupta, Pulkit; Liu, Bo; Klepacki, Dorota et al. (2016) Nascent peptide assists the ribosome in recognizing chemically distinct small molecules. Nat Chem Biol 12:153-8|
|Qiu, Hu; Girdhar, Anuj; Schulten, Klaus et al. (2016) Electrically Tunable Quenching of DNA Fluctuations in Biased Solid-State Nanopores. ACS Nano 10:4482-8|
|Ribeiro, JoÃ£o V; Bernardi, Rafael C; Rudack, Till et al. (2016) QwikMDâ€‰-â€‰Integrative Molecular Dynamics Toolkit for Novices and Experts. Sci Rep 6:26536|
|Perilla, Juan R; Hadden, Jodi A; Goh, Boon Chong et al. (2016) All-Atom Molecular Dynamics of Virus Capsids as Drug Targets. J Phys Chem Lett 7:1836-44|
|Zhang, Huilan; Hou, Guangjin; Lu, Manman et al. (2016) HIV-1 Capsid Function is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD. J Am Chem Soc :|
|Liu, Chuang; Perilla, Juan R; Ning, Jiying et al. (2016) Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. Nat Commun 7:10714|
|Stone, John E; Hallock, Michael J; Phillips, James C et al. (2016) Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. IEEE Int Symp Parallel Distrib Process Workshops Phd Forum 2016:89-100|
|Zhang, Yi; Schulten, Klaus; Gruebele, Martin et al. (2016) Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide. Biophys J 110:1744-52|
|Stone, John E; Sener, Melih; Vandivort, Kirby L et al. (2016) Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing. Parallel Comput 55:17-27|
|Stone, John E; Sherman, William R; Schulten, Klaus (2016) Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering. IEEE Int Symp Parallel Distrib Process Workshops Phd Forum 2016:1048-1057|
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