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ot14@columbia.edu
Software:
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AutoDock Vina: is an open-source program for doing molecular docking. It is perhaps the most popular docking program today, with over 4000 citations. I designed and implemented it, but please note that I no longer work at Scripps or provide support for AutoDock Vina. Follow this link instead, if you have questions.
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O'Chess: a hobby project of mine and probably one of the shortest complete chess programs. O'Chess is written in O'Caml.
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Predict S2: artificial neural network-based prediction of local protein rigidity from structure.
Publications (Google Scholar):
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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
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O. Trott, K. Siggers, B. Rost, A. G. Palmer,
Protein conformational flexibility prediction using machine learning,
Journal of Magnetic Resonance 192 (2008) 37-47
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O. Trott,
Ph.D. Thesis: Protein dynamics and its prediction using machine learning,
Columbia University (2004)
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O. Trott, A. G. Palmer,
Theoretical study of R1ρ rotating-frame and R2 free-precession relaxation in the presence of n-site chemical exchange,
Journal of Magnetic Resonance 170 (2004) 104-112
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O. Trott, D. Abergel, A. G. Palmer,
An average-magnetization analysis of R1ρ relaxation outside of the fast-exchange limit,
Molecular Physics 101-6 (2003) 753-763
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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
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O. Trott, A. G. Palmer,
R1ρ relaxation outside of the fast-exchange limit,
Journal of Magnetic Resonance 154 (2002) 157-160
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