Group highlights

(For a full list see below or go to Google Scholar.)

cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational Approach

M. Benton, M. Furr, V. Govind Kumar, A. Polasa, F. Gao, C-D Heyes, T-K Suresh Kumar, M. Moradi

J.Chem. Inf. Model, vol. 63, pp. 4125–4137, 2023

Developing a Rational Approach to Designing Recombinant Proteins for Peptide-Directed Nanoparticle Synthesis

A. Polasa, I. Mosleh, J. Losey, A. Abbaspourrad, R. Beitle and M. Moradi

Nanoscale Adv., vol. 4, pp. 3161–3171, 2022

Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters

S. Sauve, J.Williamson, A. Polasa and M. Moradi

Membranes, vol. 13, pp. 462, 2023

Prefusion Spike Protein Conformational Changes Are Slower in SARS-CoV-2 than in SARS-CoV-1.

V. Govind. Kumar, D. S. Ogden, U. H. Isu, A. Polasa, J. Losey and M. Moradi

J. Biol. Chem, 298:101814, 2022.

Full List


  • A Polasa and M Moradi, Towards A Purely Physics-based Computational Binding Affinity Estimation Nature Computational Science, 3:10-11, 2023.
  • U Isu, S Badiee, E Khodadadi, M Moradi, Cholesterol in Class C GPCRs: Role, Relevance, and Localization Membranes, 13:301, 2023.
  • S Sauve, J Williamson, A Polasa, M Moradi, Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamilty of Transporters Membranes, 13:462, 2023.
  • S Badiee, U Isu, E Khodadadi, M Moradi, The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs Membranes, 13:568, 2023.
  • V Govind Kumar, A Polasa, S Agrawal, T K S Kumar, M Moradi, Binding Affinity Estimation from Restrained Umbrella Sampling Simulations Nature Computational Science, 3:59, 2023.
  • M Benton, M Furr, V Govind Kumar, A Polasa, F Gao, C-D Heyes, T-K Suresh Kumar, M Moradi cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach Journal of Chemical Information and Modeling, 2023.
  • Goolsby, Curtis; Losey, James; Fakharzadeh, Ashkan; Xu, Yuchen; Düker, Marie-Christine; Getmansky Sherman, Mila; Matteson, David; Moradi, Mahmoud; Addressing the Embeddability Problem in Transition Rate Estimation J. Phys. Chem. A 2023.


  • D Ogden and M Moradi, Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins bioRxiv
  • A Polasa and M Moradi, Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase bioRxiv
  • D Ogden, K Immadisetty, M Moradi, Conformational Transition Pathways in Major Facilitator Superfamily Transporters bioRxiv
  • J-L Losey, M Jauch, D-S Matteson, M Moradi, Simulating freely-diffusing single-molecule FRET data with consideration of protein conformational dynamics bioRxiv
  • C Goolsby, A Fakharzadeh, M Moradi, Thermodynamic and Kinetic Characterization of Protein Conformational Dynamics within a Riemannian Framework bioRxiv





  • S Burgin, J Oramous, M Kaminski, L Stocker, and M Moradi, High School Biology Students Use of VMD as an Authentic Tool for Learning about Modeling as a Professional Scientific Practice. Biochem. Mol. Biol. Educ, 46:230-236, 2018.
  • M Kiaei, M Balasubramaniam, V Govind Kumar, R J Shmookler Reis, M Moradi, and K I Varughese, ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregation. Sci. Rep., 2018 8:13102, 2018.


  • K Immadisetty, J Hettige, and M Moradi, What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT? J. Phys. Chem. B, 121:3644-3656, 2017.
  • A Singharoy, C Chipot, M Moradi, and K Schulten, Chemomechanical coupling in hexameric protein–protein interfaces harness energy within V–type ATPases. J. Am. Chem. Soc., 139:293-310, 2017.





  • M Moradi and E Tajkhorshid, Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Proc. Natl. Aca. Sci. USA, 110:18916, 2013.
    UIUCNEWS BUREAU Access the recommendation on F1000Prime
  • M Moradi, and E Tajkhorshid, Driven metadynamics: Reconstructing equilibrium free energies from driven adaptive-bias simulations. J. Phys. Chem. Lett., 4:1882, 2013.
  • M Moradi, V Babin, C Roland, and C Sagui, Reaction path ensemble of B-Z-DNA transition: A Comprehensive atomistic study. Nucleic Acids Res., 41:33, 2013.
  • M Moradi, V Babin, C Sagui, and C Roland, Recipes for free energy calculations in biomolecular systems. In Biomolecular simulations: methods and protocols. Humana Press (Springer), Methods Mol. Biol., 924:313-37, 2013.
  • M Moradi, V Babin, C Roland, and C Sagui, Free energies, structural characteristics, and transition mechanisms of proline-rich peptides. In Proline: Biosynthesis, Regulation and Health Benefits, Nova Publishers, ISBN: 978-1-62257-745-3, 2013.
  • M Kalani, A Moradi, M Moradi, E Tajkhorshid, Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. Biophys. J., 105:993, 2013.