A message passing approach to Side Chain Positioning with applications in protein docking refinement. - Mohammad Moghadasi; Dima Kozakov; Artem B. Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2012)

A new distributed algorithm for side-chain positioning in the process of protein docking. - Mohammad Moghadasi; Dima Kozakov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis (CDC, 2013)

A Subspace Semi-Definite programming-based Underestimation (SSDU) method for stochastic global optimization in protein docking. - Feng Nan; Mohammad Moghadasi; Pirooz Vakili; Sandor Vajda; Dima Kozakov; Ioannis Ch. Paschalidis (CDC, 2014)

The Impact of Side-Chain Packing on Protein Docking Refinement. - Mohammad Moghadasi; Hanieh Mirzaei; Artem B. Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch. Paschalidis; Dima Kozakov (J. Chem. Inf. Model., 2015)

Optimization methods for side-chain positioning and macromolecular docking - Mohammad Moghadasi (2015)

Focused grid-based resampling for protein docking and mapping. - Artem B. Mamonov; Mohammad Moghadasi; Hanieh Mirzaei; Shahrooz Zarbafian; Laurie E. Grove; Tanggis Bohnuud; Pirooz Vakili; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov (J. Comput. Chem., 2016)

Protein-ligand docking using FFT based sampling: D3R case study. - Dzmitry Padhorny; David R. Hall; Hanieh Mirzaei; Artem B. Mamonov; Mohammad Moghadasi; Andrey Alekseenko; Dmitri Beglov; Dima Kozakov (J. Comput. Aided Mol. Des., 2018)