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
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)
2013
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
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.