|85 BioSimLab - Publications

Publications

Group highlights

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

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

A. Polasa and M. Moradi

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

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

V Govind Kumar and M. Moradi

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

Elucidating the Molecular Basis of Spontaneous Activation in an Engineered Mechanosensitive Channel.

K Immadisetty, and M. Moradi

Comput. Struct. Biotechnol. J., 20:2539, 2022.

Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus Thermophilus

K. Immadisetty and M. Moradi

J. Phys. Chem. B August 2021

Full List

2022

  • V Govind Kumar, A Polasa, S Agrawal, T K S Kumar, M Moradi, Binding Affinity Estimation from Restrained Umbrella Sampling Simulations Accepted for publicaiton in Nature Computational Science.
  • A Polasa, J Hettige, K Immadisetty, M Moradi, An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulations Front. Mol. Biosci., 15 August 2022
  • A Polasa, I Mosleh, J Losey, A Abbaspourrad, R Beitle, M Moradi, Developing a Rational Approach to Designing Recombinant Proteins for Peptide-Directed Nanoparticle Synthesis Nanoscale Adv., vol. 4, pp. 3161–3171, 2022,https://doi.org/10.1039/D2NA00212D.
  • K Immadisetty, A Polasa, R Shelton, and M Moradi, Elucidating the Molecular Basis of Spontaneous Activation in an Engineered Mechanosensitive Channel. Comput. Struct. Biotechnol. J., 20:2539, 2022.
  • 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.

Preprint

  • 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 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
  • V Govind Kumar, S Agrawal, T-K Suresh Kumar, M Moradi Binding Affinity Estimation From Restrained Umbrella Sampling Simulations bioRxiv
  • 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

2021

2019

2018

  • 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.

2017

  • 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.

2016

2015

2014

2013

  • 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.
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  • 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.

2009-2012