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Journal of Chemical Theory and Computation|February 6, 2013
Rigid Body Energy Minimization on Manifolds for Molecular DockingHanieh Mirzaei, Dmitri Beglov, Ioannis Ch Paschalidis, et al.Biophysical Journal|November 18, 2009
Binding hot spots and amantadine orientation in the influenza a virus M2 proton channelGwo-Yu Chuang, Dima Kozakov, Ryan Brenke, et al.Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control|April 28, 2015
A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein dockingFeng Nan, Mohammad Moghadasi, Pirooz Vakili, et al.Bioinformatics (Oxford, England)|October 12, 2012
Application of asymmetric statistical potentials to antibody-protein dockingRyan Brenke, David R Hall, Gwo-Yu Chuang, et al.Nucleic Acids Research|June 19, 2012
Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehydeTanggis Bohnuud, Dmitri Beglov, Chi Ho Ngan, et al.Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control|March 17, 2015
Optimization on the space of rigid and flexible motions: an alternative manifold optimization approachPirooz Vakili, Hanieh Mirzaei, Shahrooz Zarbafian, et al.Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control|April 26, 2014
A New Approach to Rigid Body Minimization with Application to Molecular DockingHanieh Mirzaei, Dima Kozakov, Dmitri Beglov, et al.Proceedings of the National Academy of Sciences of the United States of America|August 3, 2011
Structural conservation of druggable hot spots in protein-protein interfacesDima Kozakov, David R Hall, Gwo-Yu Chuang, et al.Journal of Molecular Biology|December 22, 2019
ClusPro LigTBM: Automated Template-based Small Molecule DockingAndrey Alekseenko, Sergei Kotelnikov, Mikhail Ignatov, et al.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing|December 10, 2021
Side-chain Packing Using SE(3)-TransformerAkhil Jindal, Sergei Kotelnikov, Dzmitry Padhorny, et al.Pageof 33