Leonardo Trabuco
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I'm Leonardo Giantini Trabuco, graduate student at the Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign and working at the Theoretical and Computational Biophysics Group. Telephone: (217) 244-8946 Email: ltrabuco@ks.uiuc.edu Mailing address |
Education
B.Sc. in Molecular Sciences, University of Sao Paulo, Brazil (2005).
Research Interests
Understand the molecular mechanisms of protein synthesis on the ribosome by means of computer simulations.
Design multiscale molecular dynamics methods to allow for long-timescale simulations.
Develop multiresolution modeling methods, such as flexible fitting of atomic structures into cryo-EM maps.
Develop software for molecular modeling within VMD.
Accelerate molecular modeling applications using GPU computing.
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| Molecular Dynamics Flexible Fitting | GPU computing | Ribosome dynamics |
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Publications
Since joining TCBG:
Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software. Kirby Vandivort, James C. Phillips, Elizabeth Villa, Peter L. Freddolino, James Gumbart, Leonardo G. Trabuco, Danielle E. Chandler, Jen Hsin, Christopher B. Harrison, Laxmikant Kale, and Klaus Schulten. Proceedings of the 2008 TeraGrid Conference, 2008.
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, and Klaus Schulten. Structure, 16:673-683, 2008.
Dynamics of recognition between tRNA and elongation factor Tu. John Eargle, Alexis A. Black, Anurag Sethi, Leonardo G. Trabuco, and Zaida Luthey-Schulten. Journal of Molecular Biology, 377:1382-1405, 2008.
Accelerating molecular modeling applications with graphics processors. John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007.
Before joining TCBG:
ATP-Sensitive K+ Channels in Renal Mitochondria. Douglas V. Cancherini, Leonardo G. Trabuco, Nancy A. Reboucas, and Alicia J. Kowaltowski. American Journal of Physiology Renal Physiology 285:F1291-F1296, 2003.
Software
VMD plugins:
Salt Bridges - finds salt bridges in a trajectory (with Elizabeth Villa)
Dowser - process input files and runs DOWSER (with Emma Falck)
VMD scripts:
rmsd_matrix - calculates a matrix of RMSD between each given frame in a trajectory
residmap - converts resids between different numbering schemes
Poster presentations
Since joining TCBG:
Flexibly fitting of atomic structures into electron microscopy maps using molecular dynamics. L G. Trabuco, E. Villa, K. Mitra, J. Sengupta, J. Frank, and K. Schulten. 3DEM Gordon Conference, 2008. Il Ciocco (Barga), Italy.
Flexibly docking the ribosome into EM density data. E. Villa, L.G. Trabuco, J. Frank, and K. Schulten. Ribosomes 2007, 2007. Cape Cod, MA.
Modeling and simulation of a bacterial ribosome. L.G. Trabuco, E. Villa, E. Falck, K. Mitra, J. Frank, and K. Schulten. Ribosomes 2007, 2007. Cape Cod, MA.
Modeling and simulation of a bacterial ribosome. L.G. Trabuco, E. Falck, E. Villa, and K. Schulten. Biophysical Society Meeting, 2007. Baltimore, MD.
Before joining the TCBG: click here
Teaching
DNA case study (with Elizabeth Villa)