A new approach to rigid body minimization with application to molecular docking. - Hanieh Mirzaei; Dima Kozakov; Dmitri Beglov; Ioannis Ch. Paschalidis; Sandor Vajda; Pirooz Vakili (CDC, 2012)

Flexible refinement of protein-ligand docking on manifolds. - Hanieh Mirzaei; Elizabeth A. Villar; Scott E. Mottarella; Dmitri Beglov; Ioannis Ch. Paschalidis; Sandor Vajda; Dima Kozakov; Pirooz Vakili (CDC, 2013)

ILP formulations for variation/defect-tolerant logic mapping on crossbar nano-architectures. - Masoud Zamani; Hanieh Mirzaei; Mehdi Baradaran Tahoori (ACM J. Emerg. Technol. Comput. Syst., 2013)

Optimization on the space of rigid and flexible motions: An alternative manifold optimization approach. - Pirooz Vakili; Hanieh Mirzaei; Shahrooz Zarbafian; Ioannis Ch. Paschalidis; Dima Kozakov; Sandor Vajda (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)

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)