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Mahmoud Moradi, Ph.D. - Publications

Affiliations: 
2011 North Carolina State University, Raleigh, NC 
Area:
General Biophysics, Biochemistry
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Chen H, Ogden D, Pant S, Cai W, Tajkhorshid E, Moradi M, Roux B, Chipot C. A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls. Journal of Chemical Theory and Computation. PMID 35138832 DOI: 10.1021/acs.jctc.1c01049  0.311
2020 Moradi M. An Integrative Approach to Single-Molecule FRET Spectroscopy and Molecular Dynamics Simulations for the Study of Intrinsically Disordered Proteins Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.906  0.344
2020 Isu U, Tabari SH, Kumar VG, Moradi M. Effect of Cholesterol on the Structural Dynamics of Metabotropic Glutamate Receptor (mGluR1): A Molecular Dynamics Study Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.2885  0.309
2019 Harkey T, Govind Kumar V, Hettige J, Tabari SH, Immadisetty K, Moradi M. The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2. Scientific Reports. 9: 14451. PMID 31595020 DOI: 10.1038/S41598-019-51052-9  0.3
2019 Faouri RA, Krueger E, Govind Kumar V, Fologea D, Straub D, Alismail H, Alfaori Q, Kight A, Ray J, Henry R, Moradi M, Salamo G. An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of Lysenin. Scientific Reports. 9: 11440. PMID 31391571 DOI: 10.1038/S41598-019-47725-0  0.324
2019 Immadisetty K, Hettige J, Moradi M. Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter. Acs Central Science. 5: 43-56. PMID 30693324 DOI: 10.1021/Acscentsci.8B00480  0.32
2019 Goolsby C, Moradi M. Overcoming the Embeddability Problem: A More Robust Calculation of Kinetic Information from Sparsely Sampled Molecular Dynamics Simulations Biophysical Journal. 116: 145a. DOI: 10.1016/J.Bpj.2018.11.802  0.385
2019 Ogden DS, Govind Kumar V, Moradi M. Mechanistic Study of a Peptidase Containing ABC-Transporter, Employing Microsecond Level Molecular Dynamics Simulations and Enhanced Sampling Techniques Biophysical Journal. 116: 126a-127a. DOI: 10.1016/J.Bpj.2018.11.703  0.38
2019 Govind Kumar V, Agrawal S, Kumar T, Moradi M. A Comprehensive Investigation of the Stabilization of Monomeric Hfgf1 by Heparin Hexasaccharide using Microsecond-Level MD Simulations and Enhanced Sampling Techniques Biophysical Journal. 116: 190a-191a. DOI: 10.1016/J.Bpj.2018.11.1056  0.322
2018 Kiaei M, Balasubramaniam M, Govind Kumar V, Shmookler Reis RJ, Moradi M, Varughese KI. ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregation. Scientific Reports. 8: 13102. PMID 30166578 DOI: 10.1038/S41598-018-31199-7  0.302
2018 Moradi M, Hettige J. Lipid-Dependent Alternating Access Mechanism in ABC Exporters Revealed using Microsecond-Level Molecular Dynamics Simulations Biophysical Journal. 114: 148a. DOI: 10.1016/J.Bpj.2017.11.832  0.391
2018 Hettige J, Hamid Tabari S, Moradi M. Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Transporter: A Molecular Dynamics Study Biophysical Journal. 114: 461a. DOI: 10.1016/J.Bpj.2017.11.2543  0.341
2017 Hamid Tabari S, Hettige J, Moradi M. All-Atom Molecular Dynamics Simulation of Stealth Liposomes Biophysical Journal. 112: 75a. DOI: 10.1016/J.Bpj.2016.11.450  0.367
2017 Moradi M, Immadisetty KC, Hettige J. Couplings between Local and Global Conformational Changes in Proton-Coupled Oligopeptide Transporters Biophysical Journal. 112: 448a. DOI: 10.1016/J.Bpj.2016.11.2404  0.395
2016 Fakharzadeh A, Moradi M. Effective Riemannian Diffusion Model for Conformational Dynamics of Biomolecular Systems. The Journal of Physical Chemistry Letters. 7: 4980-4987. PMID 27973909 DOI: 10.1021/Acs.Jpclett.6B02208  0.43
2016 Immadisetty KC, Hettige JJ, Moradi M. What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT? The Journal of Physical Chemistry. B. PMID 27959539 DOI: 10.1021/Acs.Jpcb.6B09733  0.409
2016 Singharoy A, Chipot C, Moradi M, Schulten K. Chemomechanical coupling in hexameric protein-protein interfaces harness energy within V-type ATPases. Journal of the American Chemical Society. PMID 27936329 DOI: 10.1021/Jacs.6B10744  0.366
2016 Moradi M. A Riemannian Framework for Tackling Large-Scale Conformational Changes of Proteins using All-ATOM Molecular Dynamics Simulations Biophysical Journal. 110: 643a. DOI: 10.1016/J.Bpj.2015.11.3439  0.464
2015 Moradi M, Enkavi G, Tajkhorshid E. Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate:phosphate antiporter. Nature Communications. 6: 8393. PMID 26417850 DOI: 10.1038/Ncomms9393  0.374
2015 Li J, Wen PC, Moradi M, Tajkhorshid E. Computational characterization of structural dynamics underlying function in active membrane transporters. Current Opinion in Structural Biology. 31: 96-105. PMID 25913536 DOI: 10.1016/J.Sbi.2015.04.001  0.352
2015 Moradi M, Babin V, Roland C, Sagui C. The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application Journal of Physics: Conference Series. 640. DOI: 10.1088/1742-6596/640/1/012020  0.654
2015 Moradi M, Sagui C, Roland C. Calculating transition and reaction rates with nonequilibrium work measurements Journal of Physics: Conference Series. 640. DOI: 10.1088/1742-6596/640/1/012014  0.651
2015 Moradi M, Enkavi G, Tajkhorshid E. Towards Thermodynamic Characterization of Transport Cycle in Secondary Transporters using Enhanced Sampling Techniques Biophysical Journal. 108: 144a. DOI: 10.1016/J.Bpj.2014.11.797  0.385
2015 Tajkhorshid E, Moradi M, Li J, Wen P, Thangapandian S, Vermaas J. Advances in Atomic-Level Simulations of Large-Scale Functional Motions of Membrane Transporters Biophysical Journal. 108: 371a. DOI: 10.1016/J.Bpj.2014.11.2032  0.411
2014 Moradi M, Sagui C, Roland C. Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates. The Journal of Chemical Physics. 140: 034115. PMID 25669371 DOI: 10.1063/1.4861056  0.65
2014 Moradi M, Sagui C, Roland C. Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities. The Journal of Chemical Physics. 140: 034114. PMID 25669370 DOI: 10.1063/1.4861055  0.639
2014 Moradi M, Tajkhorshid E. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems. Journal of Chemical Theory and Computation. 10: 2866-2880. PMID 25018675 DOI: 10.1021/Ct5002285  0.436
2014 Hulse RE, Sachleben JR, Wen PC, Moradi M, Tajkhorshid E, Perozo E. Conformational dynamics at the inner gate of KcsA during activation. Biochemistry. 53: 2557-9. PMID 24621378 DOI: 10.1021/Bi500168U  0.347
2014 Moradi M, Sagui C, Roland C. Publisher's Note: “Investigating rare events with nonequilibrium work measurements. II. Transition and reaction rates” [J. Chem. Phys. 140, 034115 (2014)] The Journal of Chemical Physics. 140: 069902. DOI: 10.1063/1.4865582  0.595
2014 Moradi M, Sagui C, Roland C. Publisher's Note: “Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities” [J. Chem. Phys. 140, 034114 (2014)] The Journal of Chemical Physics. 140: 069901. DOI: 10.1063/1.4865580  0.601
2014 Moradi M, Tajkhorshid E. Characterizing Conformational Ensemble and Free Energy Landscape of ABC Exporters using a Novel System-Specific Sampling Approach Biophysical Journal. 106: 789a. DOI: 10.1016/J.Bpj.2013.11.4328  0.444
2014 Moradi M, Tajkhorshid E. Driven Adaptive-Bias Scheme: A Hybrid Free Energy Method for Biomolecular Systems with Complex Energy Landscapes Biophysical Journal. 106: 640a. DOI: 10.1016/J.Bpj.2013.11.3544  0.435
2014 Enkavi G, Li J, Wen P, Thangapandian S, Moradi M, Jiang T, Han W, Tajkhorshid E. A microscopic view of the mechanisms of active transport across the cellular membrane Annual Reports in Computational Chemistry. 10: 77-125. DOI: 10.1016/B978-0-444-63378-1.00004-5  0.345
2013 Moradi M, Tajkhorshid E. Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Proceedings of the National Academy of Sciences of the United States of America. 110: 18916-21. PMID 24191018 DOI: 10.1073/Pnas.1313202110  0.408
2013 Kalani MR, Moradi A, Moradi M, Tajkhorshid E. Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. Biophysical Journal. 105: 993-1003. PMID 23972851 DOI: 10.1016/J.Bpj.2013.06.047  0.387
2013 Moradi M, Tajkhorshid E. Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations. The Journal of Physical Chemistry Letters. 4: 1882-1887. PMID 23795244 DOI: 10.1021/Jz400816X  0.48
2013 Moradi M, Babin V, Roland C, Sagui C. Reaction path ensemble of the B-Z-DNA transition: a comprehensive atomistic study. Nucleic Acids Research. 41: 33-43. PMID 23104380 DOI: 10.1093/Nar/Gks1003  0.603
2013 Moradi M, Babin V, Sagui C, Roland C. Recipes for free energy calculations in biomolecular systems. Methods in Molecular Biology (Clifton, N.J.). 924: 313-37. PMID 23034754 DOI: 10.1007/978-1-62703-017-5_12  0.685
2013 Kalani MR, Moradi A, Moradi M, Tajkhorshid E. Characterizing the Molecular Mechanism of the Histidine Switch Model in Influenza Virus Hemagglutinin Biophysical Journal. 104: 68a. DOI: 10.1016/J.Bpj.2012.11.412  0.344
2013 Wen P, Moradi M, Hulse RE, Perozo E, Tajkhorshid E. Conformational Transition of KcsA Gating and the Mechanism of its pH-Dependence Biophysical Journal. 104: 25a. DOI: 10.1016/J.Bpj.2012.11.173  0.309
2013 Moradi M, Tajkhorshid E. Outward- to Inward-Facing Transition of MsbA Transporter: A Mechanistic Picture at Atomic Resolution Biophysical Journal. 104: 288a. DOI: 10.1016/J.Bpj.2012.11.1611  0.419
2013 Moradi M, Enkavi G, Tajkhorshid E. Characterizing the Pathway, Free Energy, and the Effect of Substrate Binding on Structural Transition of MFS Transporter GlpT between Inward- and Outward-Facing States Biophysical Journal. 104: 287a. DOI: 10.1016/J.Bpj.2012.11.1607  0.438
2012 Moradi M, Babin V, Roland C, Sagui C. Are long-range structural correlations behind the aggregration phenomena of polyglutamine diseases? Plos Computational Biology. 8: e1002501. PMID 22577357 DOI: 10.1371/Journal.Pcbi.1002501  0.615
2012 Moradi M, Enkavi G, Tajkhorshid E. Conformational Transition Pathway of GlpT Transporter, Characterized by Nonequilibrium Molecular Dynamics Simulations Biophysical Journal. 102: 605a-606a. DOI: 10.1016/J.Bpj.2011.11.3301  0.419
2012 Gan W, Moradi M, Tajkhorshid E. Characterizing Transition Pathways in the Transport Cycle of ABC Transporter MsbA Biophysical Journal. 102: 446a. DOI: 10.1016/J.Bpj.2011.11.2446  0.378
2011 Moradi M, Babin V, Sagui C, Roland C. PPII propensity of multiple-guest amino acids in a proline-rich environment. The Journal of Physical Chemistry. B. 115: 8645-56. PMID 21630640 DOI: 10.1021/Jp203874F  0.608
2011 Moradi M, Babin V, Sagui C, Roland C. A statistical analysis of the PPII propensity of amino acid guests in proline-rich peptides. Biophysical Journal. 100: 1083-93. PMID 21320454 DOI: 10.1016/J.Bpj.2010.12.3742  0.627
2011 Moradi M, Sagui C, Roland C. Calculating relative transition rates with driven nonequilibrium simulations Chemical Physics Letters. 518: 109-113. DOI: 10.1016/J.Cplett.2011.10.054  0.639
2010 Moradi M, Babin V, Roland C, Sagui C. A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers. The Journal of Chemical Physics. 133: 125104. PMID 20886968 DOI: 10.1063/1.3481087  0.72
2010 Moradi M, Lee JG, Babin V, Roland C, Sagui C. Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation International Journal of Quantum Chemistry. 110: 2865-2879. DOI: 10.1002/Qua.22875  0.702
2009 Moradi M, Babin V, Roland C, Darden TA, Sagui C. Conformations and free energy landscapes of polyproline peptides. Proceedings of the National Academy of Sciences of the United States of America. 106: 20746-51. PMID 19923435 DOI: 10.1073/Pnas.0906500106  0.751
2009 Babin V, Karpusenka V, Moradi M, Roland C, Sagui C. Adaptively biased molecular dynamics: An umbrella sampling method with a time-dependent potential International Journal of Quantum Chemistry. 109: 3666-3678. DOI: 10.1002/Qua.22413  0.596
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