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.
| Guo, Qiang; Lehmer, Carina; Martínez-Sánchez, Antonio et al. (2018) In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment. Cell 172:696-705.e12 |
| Mahinthichaichan, Paween; Morris, Dylan M; Wang, Yi et al. (2018) Selective Permeability of Carboxysome Shell Pores to Anionic Molecules. J Phys Chem B 122:9110-9118 |
| Kerr, Daniel; Tietjen, Gregory T; Gong, Zhiliang et al. (2018) Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins. Biochim Biophys Acta Biomembr 1860:2126-2133 |
| Ohmann, Alexander; Li, Chen-Yu; Maffeo, Christopher et al. (2018) A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes. Nat Commun 9:2426 |
| Scheurer, Maximilian; Rodenkirch, Peter; Siggel, Marc et al. (2018) PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations. Biophys J 114:577-583 |
| Sun, Chang; Benlekbir, Samir; Venkatakrishnan, Padmaja et al. (2018) Structure of the alternative complex III in a supercomplex with cytochrome oxidase. Nature 557:123-126 |
| Speltz, Thomas E; Mayne, Christopher G; Fanning, Sean W et al. (2018) A ""cross-stitched"" peptide with improved helicity and proteolytic stability. Org Biomol Chem 16:3702-3706 |
| Ma, Wen; Whitley, Kevin D; Chemla, Yann R et al. (2018) Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase. Elife 7: |
| Mahinthichaichan, Paween; Gennis, Robert B; Tajkhorshid, Emad (2018) Cytochrome aa3 Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O2 for Catalysis. Biochemistry 57:2150-2161 |
| Wen, Po-Chao; Mahinthichaichan, Paween; Trebesch, Noah et al. (2018) Microscopic view of lipids and their diverse biological functions. Curr Opin Struct Biol 51:177-186 |
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