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.
| 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 |
| Barrick, Samantha; Li, Jing; Kong, Xinyu et al. (2018) Salt bridges gate ?-catenin activation at intercellular junctions. Mol Biol Cell 29:111-122 |
| Yoo, Jejoong; Aksimentiev, Aleksei (2018) New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Phys Chem Chem Phys 20:8432-8449 |
| Cassidy, C Keith; Himes, Benjamin A; Luthey-Schulten, Zaida et al. (2018) CryoEM-based hybrid modeling approaches for structure determination. Curr Opin Microbiol 43:14-23 |
| Infield, Daniel T; Matulef, Kimberly; Galpin, Jason D et al. (2018) Main-chain mutagenesis reveals intrahelical coupling in an ion channel voltage-sensor. Nat Commun 9:5055 |
| Arnott, Patrick M; Joshi, Himanshu; Aksimentiev, Aleksei et al. (2018) Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes. Langmuir : |
Showing the most recent 10 out of 214 publications
