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)
2013
Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P.  2013.  Flexible refinement of protein-ligand docking on manifolds. 2013 IEEE 52nd Annual Conference on Decision and Control (CDC)52nd IEEE Conference on Decision and Control. :1392-1397. Download: PDF (384.37 KB)
Moghadasi M, Kozakov D, Vakili P, Vajda S, Paschalidis IC.  2013.  A new distributed algorithm for side-chain positioning in the process of protein docking. 2013 IEEE 52nd Annual Conference on Decision and Control (CDC)52nd IEEE Conference on Decision and Control. :739-744. Download: PDF (334.84 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.
2010
2008
Shen Y, Paschalidis IC, Vakili P, Vajda S.  2008.  Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes. PLoS Computational Biology. 4(10):e1000191. Download: PDF (497.62 KB)
2007
2006
Paschalidis IC, Shen Y, Vakili P, Vajda S.  2006.  Protein Docking by Exploiting Multi-dimensional Energy Funnels. IEEE 2006 International Conference of EMBS.  Download: PDF (1.25 MB); ZIP (8.05 MB)
Paschalidis IC, Shen Y, Vakili P, Vajda S.  2006.  Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. Conference Proceedings. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. :5330-5333. Download: PDF (295.9 KB)