Leo

Leonardo G. Trabuco

  • EMBO postdoctoral research fellow
  • Email: leonardo.trabuco@bioquant.uni-heidelberg.de
  • Phone: +49 6221 54 51 360
  • Im Neuenheimer Feld 267 Room 562, 69120 Heidelberg, Germany
  • View Leonardo  Trabuco's profile on LinkedIn

Education

Publications

Research articles

  1. Trabuco LG, Betts MJ, and Russell RB. Negative protein-protein interaction datasets derived from large-scale two-hybrid experiments. Methods, 58:343-348, 2012.
  2. Trabuco LG, Lise E, Petsalaki E, and Russell RB. PepSite: prediction of peptide-binding sites from protein surfaces. Nucleic Acids Res., 40(Web Server issue):W423-426, 2012.
  3. Chan KY, Trabuco LG, Schreiner E, and Schulten K. Cryo-EM modeling by the molecular dynamics flexible fitting method. Biopolymers, 97:678-686, 2012.
  4. Schreiner E, Trabuco LG, Freddolino PL, and Schulten K. Stereochemical errors and their implications for molecular dynamics simulations. BMC Bioinformatics, 12:190, 2011.
  5. Agirrezabala X, Schreiner E, Trabuco LG, Leo J, Ortiz-Meoz RF, Schulten K, Green R, and Frank J. Structural insights into cognate vs. near-cognate discrimination during decoding. EMBO J, 30:1497-1507, 2011.
  6. Li W, Trabuco LG, Schulten K, and Frank J. Molecular dynamics of EF-G during translocation. Proteins, 79:1478-1486, 2011.
  7. Trabuco LG, Schreiner E, Gumbart J, Hsin J, Villa E, and Schulten K. Applications of the molecular dynamics flexible fitting method. J Struct Biol, 173:420-427, 2011.
  8. Trabuco LG, Schreiner E, Eargle J, Cornish P, Ha T, Luthey-Schulten Z, and Schulten K. The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J Mol Biol, 402:741-760, 2010.
  9. Trabuco LG, Harrison CB, Schreiner E, and Schulten K. Recognition of the regulatory nascent chain TnaC by the ribosome. Structure, 18:627-637, 2010.
  10. Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache JP, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K, Steitz TA, and Beckmann R. Structural insight into nascent polypeptide chain-mediated translational stalling. Science, 326:1412-1415, 2009.
  11. Gumbart J, Trabuco LG, Schreiner E, Villa E, and Schulten K. Regulation of the protein-conducting channel by a bound ribosome. Structure, 17:1453-1464, 2009.
  12. Trabuco LG, Villa E, Schreiner E, Harrison CB, and Schulten K. Molecular Dynamics Flexible Fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods, 49:174-180, 2009.
  13. Hsin J, Gumbart J, Trabuco LG, Villa E, Qian P, Hunter CN, and Schulten K. Protein-induced membrane curvature investigated through molecular dynamics flexible fitting. Biophys J, 97:321-329, 2009.
  14. Sener MK, Hsin J, Trabuco LG, Villa E, Qian P, Hunter CN, and Schulten K. Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides. Chem Phys, 357:188-197, 2009.
  15. Villa E, Sengupta J, Trabuco LG, LeBarron J, Baxter WT, Shaikh TR, Grassucci RA, Nissen P, Ehrenberg M, Schulten K, and Frank J. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proc Natl Acad Sci USA, 106:1063-1068, 2009.
  16. Trabuco LG, Villa E, Mitra K, Frank J, and Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure, 16:673-683, 2008.
  17. Eargle J, Black AA, Sethi A, Trabuco LG, and Luthey-Schulten Z. Dynamics of recognition between tRNA and elongation factor Tu. J Mol Biol, 377:1382-1405, 2008.
  18. Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, and Schulten K. Accelerating molecular modeling applications with graphics processors. J Comput Chem, 28:2618-2640, 2007.
  19. Cancherini DV, Trabuco LG, Reboucas NA, and Kowaltowski AJ. ATP-Sensitive K+ Channels in Renal Mitochondria. Am J Physiol Renal Physiol, 285:F1291-F1296, 2003.

Other publications

  1. Gumbart J, Schreiner E, Trabuco LG, Chan KY, and Schulten K. Viewing the mechanisms of translation through the computational microscope. In Joachim Frank, editor, Molecular Machines in Biology, chapter 8, pp. 142-157. Cambridge University Press, 2011.
  2. Vandivort K, Phillips JC, Villa E, Freddolino PL, Gumbart J, Trabuco LG, Chandler DE, Hsin J, Harrison CB, Kale L, and Schulten K. Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software. Proceedings of the 2008 TeraGrid Conference, 2008.