OLEG TROTT, Ph.D. Columbia University



  • AutoDock Vina: is an open-source program for doing molecular docking. It is perhaps the most popular docking program today, with over 10,000 citations. While I designed and implemented it, note that I no longer work at Scripps or provide support for AutoDock Vina. Please follow this link instead, if you have questions.
  • O'Chess: a hobby project of mine and probably one of the shortest complete chess programs. O'Chess is written in O'Caml caml
  • Predict S2: artificial neural network-based prediction of local protein rigidity from structure.

Publications (Google Scholar):

  • O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461
  • O. Trott, K. Siggers, B. Rost, A. G. Palmer, Protein conformational flexibility prediction using machine learning, Journal of Magnetic Resonance 192 (2008) 37-47
  • O. Trott, Ph.D. Thesis: Protein dynamics and its prediction using machine learning, Columbia University (2004) pdf
  • O. Trott, A. G. Palmer, Theoretical study of R rotating-frame and R2 free-precession relaxation in the presence of n-site chemical exchange, Journal of Magnetic Resonance 170 (2004) 104-112
  • O. Trott, D. Abergel, A. G. Palmer, An average-magnetization analysis of R relaxation outside of the fast-exchange limit, Molecular Physics 101-6 (2003) 753-763
  • L. Vugmeyster, O. Trott, C. J. McKnight, D. P. Raleigh, A. G. Palmer, Temperature-dependent dynamics of the villin headpiece helical subdomain, an unusually small thermostable protein, Journal of Molecular Biology 320 (2002) 841-854
  • O. Trott, A. G. Palmer, R relaxation outside of the fast-exchange limit, Journal of Magnetic Resonance 154 (2002) 157-160