Mechanisms of amphipathic helical peptide denaturation by guanidinium chloride and urea: a molecular dynamics simulation study. - Faramarz Mehrnejad; Mahmoud Khadem-Maaref; Mohammad Mehdi Ghahremanpour; Farahnoosh Doustdar (J. Comput. Aided Mol. Des., 2010)

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program. - Mohammad Mehdi Ghahremanpour; Seyed Shahriar Arab; Saman Biook Aghazadeh; Jin Zhang; David van der Spoel (Bioinform., 2014)

Computation of Absolute Binding Free Energies for Noncovalent Inhibitors with SARS-CoV-2 Main Protease. - Mohammad Mehdi Ghahremanpour; Anastasia Saar; Julian Tirado-Rives; William L. Jorgensen (J. Chem. Inf. Model., 2023)

Assessing Metadynamics and Docking for Absolute Binding Free Energy Calculations Using Severe Acute Respiratory Syndrome Coronavirus 2 Main Protease Inhibitors. - Anastasia Saar; Mohammad Mehdi Ghahremanpour; Julian Tirado-Rives; William L. Jorgensen (J. Chem. Inf. Model., 2023)

Ensemble Geometric Deep Learning of Aqueous Solubility. - Mohammad Mehdi Ghahremanpour; Anastasia Saar; Julian Tirado-Rives; William L. Jorgensen (J. Chem. Inf. Model., 2023)