Papers+Conferences

2016
Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE, Bohnuud T, Vakili P, Paschalidis IC, Vajda S, Kozakov D.  2016.  Focused grid-based resampling for protein docking and mapping. Journal of Computational Chemistry. 37(11):961-970. Download: PDF (673.58 KB)
2015
Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D, Vajda S, Paschalidis IC, Vakili P, Kozakov D.  2015.  Energy Minimization on Manifolds for Docking Flexible Molecules. Journal of Chemical Theory and Computation. 11(3):1063-1076. Download: PDF (5.51 MB)
Moghadasi M, Mirzaei H, Mamonov A, Vakili P, Vajda S, Paschalidis IC, Kozakov D.  2015.  The Impact of Side-Chain Packing on Protein Docking Refinement. Journal of Chemical Information and Modeling. :150324100758004. Download: PDF (3.53 MB)
2014
Chowdhury R, Beglov D, Moghadasi M, Paschalidis IC, Vakili P, Vajda S, Bajaj C, Kozakov D.  2014.  Efficient Maintenance and Update of Nonbonded Lists in Macromolecular Simulations. Journal of Chemical Theory and Computation. :140926082652006. Download: PDF (2.01 MB)
Vakili P, Mirzaei H, Zarbafian S, Paschalidis IC, Kozakov D, Vajda S.  2014.  Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. 2014 IEEE 53rd Annual Conference on Decision and Control (CDC)53rd IEEE Conference on Decision and Control. :5825-5830. Download: PDF (473.3 KB)
2012
Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D.  2012.  Rigid Body Energy Minimization on Manifolds for Molecular Docking. Journal of Chemical Theory and Computation. 8(11):4374-4380.
Mirzaei H, Beglov D, Paschalidis IC, Vajda S, Vakili P, Kozakov D.  2012.  Rigid Body Energy Minimization on Manifolds for Molecular Docking. Journal of Chemical Theory and Computation. :120821123549006. Download: PDF (317.26 KB)
Moghadasi M, Kozakov D, Mamonov AB, Vakili P, Vajda S, Paschalidis IC.  2012.  A message passing approach to Side Chain Positioning with applications in protein docking refinement. 2012 IEEE 51st Annual Conference on Decision and Control (CDC)2012 IEEE 51st IEEE Conference on Decision and Control (CDC). :2310-2315.
Mirzaei H, Kozakov D, Beglov D, Paschalidis IC, Vajda S, Vakili P.  2012.  A new approach to rigid body minimization with application to molecular docking. 2012 IEEE 51st Annual Conference on Decision and Control (CDC)2012 IEEE 51st IEEE Conference on Decision and Control (CDC). :2983-2988.