CHBC Faculty Publications

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Author: Moradi, Mahmoud

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TitlePublication NamePub. TypeYear
Integration of smFRET and molecular dynamics to characterize conformational dynamics of the spike protein of wild-type SARS-CoV-2 and its variantsBiophysical JournalAbstract2023
Atomic-level characterization of the human immunodeficiency virus type 1 envelope glycoproteins using molecular dynamic simulationsBiophysical JournalAbstract2023
Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channelBiophysical JournalAbstract2023
An integrative approach to molecular dynamics and single molecule FRET techniquesBiophysical JournalAbstract2023
Cholesterol concentration effect on bilayer membranes and its role in designing efficient liposomal drug delivery systemsBiophysical JournalAbstract2023
Cholesterol dependence on the conformational changes of metabotropic glutamate receptor 1 (mGLuR1)Biophysical JournalAbstract2023
Structural effects of ALS-associated mutations on profilingBiophysical JournalAbstract2023
Comparison of cyclic AMP binding activity within HCN channel subfamily using atomistic molecular dynamics simulations of isolated cyclic nucleotide binding domainsBiophysical JournalAbstract2023
A molecular dynamics study of the FGF1/FGF2 heterodimer in human fibroblastsBiophysical JournalAbstract2023
cpSRP43 Is Both Highly Flexible and Stable: Structural Insights Using a Combined Experimental and Computational ApproachJournal of Chemical Information and ModelingJournal Article2023
Addressing the Embeddability Problem in Transition Rate EstimationJournal of Physical Chemistry AJournal Article2023
Cholesterol in Class C GPCRs: Role, Relevance, and LocalizationMembranesJournal Article2023
The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial HomologsMembranesJournal Article2023
Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of TransportersMembranesJournal Article2023
Binding affinity estimation from restrained umbrella sampling simulationsNature Computational ScienceJournal Article2023
Towards a purely physics-based computational binding affinity estimationNature Computational ScienceJournal Article2023
Developing a rational approach to designing recombinant proteins for peptide-directed nanoparticle synthesisNanoscale AdvancesJournal Article2022
A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and PitfallsJournal of Chemical Theory and ComputationJournal Article2022
An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulationsFrontiers in Molecular BiosciencesJournal Article2022
Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1Journal of Biological ChemistryJournal Article2022
Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteinsbioRxivJournal Article2022
Elucidating the molecular basis of spontaneous activation in an engineered mechanosensitive channelComputational and Structural Biotechnology JournalJournal Article2022
Physics-based computational framework for absolute binding affinity estimationAbstracts of Papers of the American Chemical SocietyAbstract2022
An investigation of the YidC-mediated membrane insertion of Pf3 coat protein using molecular dynamics simulationsBiophysical JournalAbstract2022
Addressing the embeddability problem in transition rate estimation from Markov state modelsBiophysical JournalAbstract2022
Simulating freely-diffusing single-molecule FRET data with consideration of protein conformational dynamicsBiophysical JournalAbstract2022
Characterizing the roles of chemo-mechanical couplings in the differential behavior of SARS-CoV-1 and SARS-CoV-2 spike glycoproteinBiophysical JournalAbstract2022
Structural dynamics of prefusion spike protein of SARS-CoV-2 and its variantsBiophysical JournalAbstract2022
Using molecular dynamics simulations to characterize the structural/conformational effect of amino acid substitutions at the second position of the intrinsically disordered mitochondrial localization peptide (MLP)Biophysical JournalAbstract2022
Molecular dynamics investigation of the ph-dependent influenza hemagglutinin conformational changeBiophysical JournalAbstract2022
Developing Efficient Transfer Free Energy Calculation Methods for Hydrophobicity PredictionsBiophysical JournalAbstract2021
Conformational Transition Pathway of GkPOTBiophysical JournalAbstract2021
Differential Dynamic Behavior of Prefusion Spike Glycoproteins of Sars Coronaviruses 1 and 2Biophysical JournalAbstract2021
Integrating Molecular Dynamics and smFRET Data to Study the Conformational Ensemble of the C-Terminus of Albino3 ProteinBiophysical JournalAbstract2021
An Investigation of the Conformational Dynamics of ABC Exporter PCAT1 using Microsecond-Level MD SimulationsBiophysical JournalAbstract2021
Comparing the Dynamic Differences between X-ray and Cryo-EM Structures of Cannabinoid Receptor 1 using Molecular Dynamics SimulationsBiophysical JournalAbstract2021
Molecular Dynamics Investigation of the Influenza Hemagglutinin Conformational ChangesBiophysical JournalAbstract2021
An Investigation of the Disulfide Bridge Formation of a Thylakoid Protease using Nanosecond-Level MD SimulationsBiophysical JournalAbstract2021
Investigation of Cyclic AMP Binding Interactions with Isolated Cyclic Nucleotide Binding Domain of HCN1 Channel using Atomistic Molecular Dynamics Simulations at Microsecond TimescaleBiophysical JournalAbstract2021
Differential thermodynamics and kinetics of prefusion spike proteins of SARS-CoV-1 and 2.Abstracts of Papers of the American Chemical SocietyAbstract2021
Conformational free energy landscape of prefusion spike protein in SARS-CoV-1 and 2.Abstracts of Papers of the American Chemical SocietyAbstract2021
Similarities and differences of conformational transition pathways in uniporters, symporters, and antiporters of the major facilitator superfamily of transporters.Abstracts of Papers of the American Chemical SocietyAbstract2021
Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin BindingJournal of Physical Chemistry BJournal Article2021
Mechanistic Picture for Chemomechanical Coupling in a Bacterial Proton-Coupled Oligopeptide Transporter from Streptococcus ThermophilusJournal of Physical Chemistry BJournal Article2021
Structural Propensity in the C-terminal domain of the Albino3 translocase in thylakoidsProtein ScienceAbstract2021
Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factorScientific ReportsJournal Article2021
Transient local secondary structure in the intrinsically disordered C-term of the Albino3 insertaseBiophysical JournalJournal Article2021
Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions.Structure and Function of Membrane ProteinsBook Section2021
Structural Propensity in the C-terminal Domain of the ALbino3 Translocase in ThylakoidsFASEB JournalAbstract2020
Differential dynamic behavior of prefusion spike proteins of SARS coronaviruses 1 and 2bioRxivJournal Article2020
An Investigation of the YidC-Mediated Membrane Insertion of a Pf3 Coat Protein Using MD SimulationsBiophysical JournalAbstract2020
An Integrative Approach to Single-Molecule FRET Spectroscopy and Molecular Dynamics Simulations for the Study of Intrinsically Disordered ProteinsBiophysical JournalAbstract2020
An Investigation of the Influenza Hemagglutinin Membrane Fusion Process using Microsecond-Level MD SimulationsBiophysical JournalAbstract2020
Effect of Cholesterol on the Structural Dynamics of Metabotropic Glutamate Receptor (mGluR(1)): A Molecular Dynamics StudyBiophysical JournalAbstract2020
Binding Free Energy Calculations of NMDA Glutamate ReceptorsBiophysical JournalAbstract2019
Mechanistic Study of a Peptidase Containing ABC-Transporter, Employing Microsecond Level Molecular Dynamics Simulations and Enhanced Sampling TechniquesBiophysical JournalAbstract2019
A Comprehensive Investigation of the Stabilization of Monomeric Hfgf1 by Heparin Hexasaccharide using Microsecond-Level MD Simulations and Enhanced Sampling TechniquesBiophysical JournalAbstract2019
Elucidating the Molecular Basis of pH-Triggered Activation of an Engineered Mechanosensitive ChannelBiophysical JournalAbstract2019
Overcoming the Embeddability Problem: A More Robust Calculation of Kinetic Information from Sparsely Sampled Molecular Dynamics SimulationsBiophysical JournalAbstract2019
Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC ExporterACS Central ScienceJournal Article2019
The Role of a Crystallographically Unresolved Cytoplasmic Loop in Stabilizing the Bacterial Membrane Insertase YidC2Scientific ReportsJournal Article2019
An Effective Electric Dipole Model for Voltage-induced Gating Mechanism of LyseninScientific ReportsJournal Article2019
ALS-causing mutations in profilin-1 alter its conformational dynamics: A computational approach to explain propensity for aggregationScientific ReportsJournal Article2018
High school biology students use of visual molecular dynamics as an authentic tool for learning about modeling as a professional scientific practiceBiochemistry and Molecular Biology EducationJournal Article2018
Lipid-Dependent Alternating Access Mechanism in ABC Exporters Revealed using Microsecond-Level Molecular Dynamics SimulationsBiophysical JournalAbstract2018
Microsecond-Level Simulations Reveal Membrane Protein Insertion Mechanism of Insertase YidCBiophysical JournalAbstract2018
All-Atom Molecular Dynamics Simulation of Stealth LiposomesBiophysical JournalAbstract2017
Couplings between Local and Global Conformational Changes in Proton-Coupled Oligopeptide TransportersBiophysical JournalAbstract2017
Modeling the atomistic structure and dynamics of the chloroplast signal recognition particlesAbstracts of Papers of the American Chemical SocietyAbstract2017
Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPasesJournal of the American Chemical SocietyJournal Article2017
What Can and Cannot Be Learned from Molecular Dynamics Simulations of Bacterial Proton-Coupled Oligopeptide Transporter GkPOT?Journal of Physical Chemistry BJournal Article2017
Effective Riemannian Diffusion Model for Conformational Dynamics of Biomolecular SystemsJournal of Physical Chemistry LettersJournal Article2016
Conformational free energy landscape of inward- and outward-facing states of peptidase-containing ATP-binding cassette transporter PCAT1Abstracts of Papers of the American Chemical SocietyAbstract2016
A Riemannian Framework for Tackling Large-Scale Conformational Changes of Proteins using All-ATOM Molecular Dynamics SimulationsBiophysical JournalAbstract2016
Effective Riemannian diffusion model for conformational dynamics of membrane transportersAbstracts of Papers of the American Chemical SocietyAbstract2015