The Biomedical Technology Research Resource for Macromolecular Modeling and Bioinformatics, hereafter referred to simply as the ?Center,? develops software tools to model cellular processes at both the atomic and coarse- grained level. An experienced, multidisciplinary team of researchers at the Center provides for the biomedical research community a ?computational microscope? and collaborates with leading experimental laboratories. The computational microscope, equipped with molecular visualization, sequence, structure and dynamics analysis capabilities, presently consists of NAMD, VMD, and Lattice Microbes software programs that are free and open- source. 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 goals: Raise performance, e?ciency, and accuracy of simulations for cellular processes at long time and large length scales; Facilitate innovation in the biomedical research community by providing accessible simulation tools support- ing, in particular, advanced multi-copy enhanced sampling protocols, QM/MM, multi-resolution methods, coarse-grained models, stochastic simulations of large networks of biochemical reactions, Brownian dynamics, and whole cell simulations; Lead the implementation of state of the art technologies in GPU, petascale, and pre-exascale computing into biomedical research at the molecular and cellular level; Support visualization and analysis of biomolecular systems with powerful, customizable software packages, integrating multi-modal experimental imaging (e.g., cryo-electron microscopy and tomography, X-ray, NMR) and -omics data with model building and simulation tools; Enhance performance for visualization, analysis, and modeling of large-size and long-timescale cellular pro- cesses by exploiting emerging technologies such as GPU acceleration, remote visualization, and non-volatile memory; Develop methods to model whole cell behavior and large cellular components such as membrane environments and chromatin; 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 with the use of electronic text books and videos, providing a cutting edge computational laboratory, cloud computing resources, hands-on training, ?rst-rate educational material, and an extensive, widely-used website to biomedical researchers.

Public Health Relevance

The Biomedical Technology Research Resource for Macromolecular Modeling and Bioinformatics pioneers computer- based biomedical research into cellular processes. The Resource makes emerging computational technologies avail- able for fundamental biomedical research, develops powerful simulation tools for biomolecular and whole cell processes related to health and disease, and provides its open-source software tools to its collaborators and the greater biomedical community for the purpose of developing new diagnostic tools and drug treatments. The Re- source trains biomedical researchers in the use of its tools through tutorials and regular hands-on workshops where participants also obtain support in carrying out their own research problems.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Biotechnology Resource Grants (P41)
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Special Emphasis Panel (ZRG1)
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Krepkiy, Dmitriy
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University of Illinois Urbana-Champaign
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United States
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Milles, Lukas F; Schulten, Klaus; Gaub, Hermann E et al. (2018) Molecular mechanism of extreme mechanostability in a pathogen adhesin. Science 359:1527-1533
Carnevale, Lauren N; Arango, Andres S; Arnold, William R et al. (2018) Endocannabinoid Virodhamine Is an Endogenous Inhibitor of Human Cardiovascular CYP2J2 Epoxygenase. Biochemistry 57:6489-6499
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:

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