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Author Details

Michael Feig
Michigan State University
1998
150
47
Andrej Sali (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
38000367One bead per residue can describe all-atom protein structures.Structure2024
36607820Modeling Concentration-dependent Phase Separation Processes Involving Peptides and RNA via Residue-Based Coarse-Graining.J Chem Theory Comput2023
37325682The effect of polymer length in liquid-liquid phase separation.Cell Rep Phys Sci2023
36947548Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine learning.PLoS Comput Biol2023
37098073Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease.PLoS Comput Biol2023
36774359Direct generation of protein conformational ensembles via machine learning.Nat Commun2023
35219215Protein assembly and crowding simulations.Curr Opin Struct Biol2022
35510704Multi-state modeling of G-protein coupled receptors at experimental accuracy.Proteins2022
35471152Inhibitory proteins block substrate access by occupying the active site cleft of <i>Bacillus subtilis</i> intramembrane protease SpoIVFB.Elife2022
36440862Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions.J Phys Chem B2022
36279257Characterizing Transient Protein-Protein Interactions by Trp-Cys Quenching and Computer Simulations.J Phys Chem Lett2022
33200457New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems.J Comput Chem2021
33562962Improved Sampling Strategies for Protein Model Refinement Based on Molecular Dynamics Simulation.J Chem Theory Comput2021
33496264Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments.Elife2021
34587746Virtual Issue on Protein Crowding and Stability.J Phys Chem B2021
34428995Biosynthesis and trafficking of heme <i>o</i> and heme <i>a</i>: new structural insights and their implications for reaction mechanisms and prenylated heme transfer.Crit Rev Biochem Mol Biol2021
34156124Physics-based protein structure refinement in the era of artificial intelligence.Proteins2021
34270995Crowding affects structural dynamics and contributes to membrane association of the NS3/4A complex.Biophys J2021
34215742Reduced efficacy of a Src kinase inhibitor in crowded protein solution.Nat Commun2021
32511334Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement.bioRxiv2020
31875339Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units.J Comput Chem2020
31693199High-accuracy protein structures by combining machine-learning with physics-based refinement.Proteins2020
31945187The endoplasmic reticulum acetyltransferases ATase1/NAT8B and ATase2/NAT8 are differentially regulated to adjust engagement of the secretory pathway.J Neurochem2020
32717410Crowded environment affects the activity and inhibition of the NS3/4A protease.Biochimie2020
32284601Short disordered protein segment regulates cross-species transmission of a yeast prion.Nat Chem Biol2020
30560249Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments.Phys Chem Chem Phys2019
31740611Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending.Proc Natl Acad Sci U S A2019
31299173Whole-Cell Models and Simulations in Molecular Detail.Annu Rev Cell Dev Biol2019
31491077Thermal Stability of Peptide Nucleic Acid Complexes.J Phys Chem B2019
31572730Modeling Crowded Environment in Molecular Simulations.Front Mol Biosci2019
31197841Driven to near-experimental accuracy by refinement via molecular dynamics simulations.Proteins2019
30945633The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy.Elife2019
30540459Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning.J Chem Inf Model2019
28975670What makes it difficult to refine protein models further via molecular dynamics simulations?Proteins2018
30224053Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It.Biophys J2018
30613205Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments.J Phys Conf Ser2018
30613206High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations.J Phys Conf Ser2018
30530696Experimental accuracy in protein structure refinement via molecular dynamics simulations.Proc Natl Acad Sci U S A2018
30555686Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.BMC Biophys2018
29675899Structure refinement of membrane proteins via molecular dynamics simulations.Proteins2018
29529244High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization.Nucleic Acids Res2018
29791152Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.J Chem Theory Comput2018
29126101PREFMD: a web server for protein structure refinement via molecular dynamics simulations.Bioinformatics2018
27819658CHARMM36m: an improved force field for folded and intrinsically disordered proteins.Nat Methods2017
30613211Computational protein structure refinement: Almost there, yet still so far to go.Wiley Interdiscip Rev Comput Mol Sci2017
28160300Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.J Comput Chem2017
28475346Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.J Chem Theory Comput2017
28242207Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.Biochim Biophys Acta Gene Regul Mech2017
28992696Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.J Chem Theory Comput2017
29155578Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.J Chem Inf Model2017
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Collaborators

Lim Heo
Michigan State University
Co-authored papers 17
Charles L Brooks
University of Michigan ann arbor
Co-authored papers 16
Andras Fiser
Albert Einstein College of Medicine
Co-authored papers 1
David A Case
Rutgers University
Co-authored papers 1
Chenxi Qiu
Harvard Medical School
Co-authored papers 1
Andrej Sali (CM4AI)
University of California San Francisco
Co-authored papers 1
Timothy S Carey
University of North Carolina at Chapel Hill
Co-authored papers 1
Mikhail Kashlev
Co-authored papers 1
Martin Zacharias
Co-authored papers 1
Martin Karplus
Harvard University
Co-authored papers 1
Koichi Takahashi
RIKEN Center for Biosystems Dynamics Research
Co-authored papers 1
Craig D Kaplan
University of Pittsburgh
Co-authored papers 1
Aaron R Dinner
James Franck Institute, Institute for Biophysical Dynamics, University of Chicago
Co-authored papers 1
Gaurav D Moghe
Cornell University
Co-authored papers 1
Corinna Burger
University of Wisconsin-Madison
Co-authored papers 1
Release 1.2