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Page 1
Protein-ligand docking using FFT based sampling: D3R case study.
Padhorny D, Hall DR, Mirzaei H, Mamonov AB, Moghadasi M, Alekseenko A, Beglov D, Kozakov D. Padhorny D, et al. Among authors: mirzaei h. J Comput Aided Mol Des. 2018 Jan;32(1):225-230. doi: 10.1007/s10822-017-0069-7. Epub 2017 Nov 3. J Comput Aided Mol Des. 2018. PMID: 29101520 Free PMC article.
Focused grid-based resampling for protein docking and mapping.
Mamonov AB, Moghadasi M, Mirzaei H, Zarbafian S, Grove LE, Bohnuud T, Vakili P, Ch Paschalidis I, Vajda S, Kozakov D. Mamonov AB, et al. Among authors: mirzaei h. J Comput Chem. 2016 Apr 30;37(11):961-70. doi: 10.1002/jcc.24273. Epub 2016 Feb 2. J Comput Chem. 2016. PMID: 26837000 Free PMC article.
Energy Minimization on Manifolds for Docking Flexible Molecules.
Mirzaei H, Zarbafian S, Villar E, Mottarella S, Beglov D, Vajda S, Paschalidis ICh, Vakili P, Kozakov D. Mirzaei H, et al. J Chem Theory Comput. 2015 Mar 10;11(3):1063-76. doi: 10.1021/ct500155t. J Chem Theory Comput. 2015. PMID: 26478722 Free PMC article.
The impact of side-chain packing on protein docking refinement.
Moghadasi M, Mirzaei H, Mamonov A, Vakili P, Vajda S, Paschalidis ICh, Kozakov D. Moghadasi M, et al. Among authors: mirzaei h. J Chem Inf Model. 2015 Apr 27;55(4):872-81. doi: 10.1021/ci500380a. Epub 2015 Mar 24. J Chem Inf Model. 2015. PMID: 25714358 Free PMC article.
Flexible Refinement of Protein-Ligand Docking on Manifolds.
Mirzaei H, Villar E, Mottarella S, Beglov D, Paschalidis IC, Vajda S, Kozakov D, Vakili P. Mirzaei H, et al. Proc IEEE Conf Decis Control. 2013:1392-1397. doi: 10.1109/CDC.2013.6760077. Proc IEEE Conf Decis Control. 2013. PMID: 24830567 Free PMC article.