V Govind Kumar, D-S Ogden, U-H Isu, A Polasa, J-L Losey, and M Moradi, Prefusion Spike Protein Conformational Changes Are Slower in SARS-CoV-2 than in SARS-CoV-1. J. Biol. Chem, 298:101814, 2022.
H Chen, D Ogden, S Pant, W Cai, E Tajkhorshid, M Moradi, B Roux, and C Chipot, A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls J. Chem. Theory Comput., 18:1406–1422, 2022.
A Polasa and M Moradi, Deciphering the Inter-domain Decoupling in the Gram-negative Bacterial Membrane Insertase bioRxiv
C Goolsby and M Moradi, Addressing the embeddability problem in transition rate estimation. bioRxiv
D Ogden, K Immadisetty, M Moradi,
Conformational Transition Pathways in Major Facilitator Superfamily TransportersbioRxiv
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,
V Govind Kumar, S Agrawal, T-K Suresh Kumar, M Moradi Binding Affinity Estimation From Restrained Umbrella Sampling SimulationsbioRxiv
M Benton, M Furr, V Govind Kumar, 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. bioaRxiv
D-R Baucom, M Furr, V Govind Kumar, P Okoto, J-L Losey, R-L Henry, M Moradi, T-K Suresh Kumar, C-D Heyes
Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertase
Biophys. J, 120:4992-5004, 2021.
K Immadisetty and M Moradi
Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus
J. Phys. Chem. B, 125:9738–9750, 2021.
S Agrawal, V Govind Kumar, R-K Gundampati, M Moradi & T-K Suresh Kumar,
Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fbroblast growth factor
Sci. Rep., 11:15579, 2021.
T Harkey, V Govind Kumar, J Hettige, S H Tabari, K Immadisetty, and M Moradi, The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2. Sci. Rep., 9:14451, 2019.
R Al Faouri, E Krueger, V Kumar, D Fologea, D Straub, H Alismail, Q Alfaori, A Kight, J Ray, R Henry, M Moradi, and G Salamo, An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of Lysenin. Sci. Rep., 9:11440, 2019.
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.
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.