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Michael Feig

Department of Biochemistry and Molecular Biology

BCH 218 | web site |

  • Molecular dynamics simulations of biomolecular systems
  • Coarse-grained modeling
  • Effects of crowded cellular environments
  • RNA polymerase function
  • Interactions of biomolecules with membranes
  • Protein structure prediction and refinement
  • Modeling of chromosomal DNA

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Recent Publications

Whole-Cell Models and Simulations in Molecular Detail.
Feig M, Sugita Y.
Annu Rev Cell Dev Biol (2019) Jul 12 .

Driven to near-experimental accuracy by refinement via molecular dynamics simulations.
Heo L, Arbour CF, Feig M.
Proteins (2019) Jun 14 .

The phage L capsid decoration protein has a novel OB-fold and an unusual capsid binding strategy.
Newcomer RL, Schrad JR, Gilcrease EB, Casjens SR, Feig M, Teschke CM, Alexandrescu AT, Parent KN.
Elife (2019) Apr 4.

Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning.
Brocke SA, Degen A, MacKerell AD Jr, Dutagaci B, Feig M.
J Chem Inf Model (2019) Mar 25; 59(3):1147-1162.

Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments.
Nawrocki G, Karaboga A, Sugita Y, Feig M.
Phys Chem Chem Phys (2019) Jan 2; 21(2):876-883.

Experimental accuracy in protein structure refinement via molecular dynamics simulations.
Heo L, Feig M.
Proc Natl Acad Sci U S A (2018) Dec 26; 115(52):13276-13281.

High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations.
Yu I, Feig M, Sugita Y.
J Phys Conf Ser (2018).

Challenges and opportunities in connecting simulations with experiments via molecular dynamics of cellular environments.
Feig M, Nawrocki G, Yu I, Wang PH, Sugita Y.
J Phys Conf Ser (2018).

Role of protein interactions in stabilizing canonical DNA features in simulations of DNA in crowded environments.
Yildirim A, Brenner N, Sutherland R, Feig M.
BMC Biophys (2018) 11:8.

Intramolecular Diffusion in α-Synuclein: It Depends on How You Measure It.
Woodard J, Srivastava KR, Rahamim G, Grupi A, Hogan S, Witalka DJ, Nawrocki G, Haas E, Feig M, Lapidus LJ.
Biophys J (2018) Oct 2; 115(7):1190-1199.

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.
JasiƄski M, Feig M, Trylska J.
J Chem Theory Comput (2018) Jul 10; 14(7):3603-3620.

Structure refinement of membrane proteins via molecular dynamics simulations.
Dutagaci B, Heo L, Feig M.
Proteins (2018) Jul; 86(7):738-750.

High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization.
Yildirim A, Feig M.
Nucleic Acids Res (2018) May 4; 46(8):3937-3952.

PREFMD: a web server for protein structure refinement via molecular dynamics simulations.
Heo L, Feig M.
Bioinformatics (2018) Mar 15; 34(6):1063-1065.

What makes it difficult to refine protein models further via molecular dynamics simulations?
Heo L, Feig M.
Proteins (2018) Mar; 86 Suppl 1:177-188.

Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model.
Dutagaci B, Feig M.
J Chem Inf Model (2017) Dec 26; 57(12):3032-3042.

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation.
Nawrocki G, Wang PH, Yu I, Sugita Y, Feig M.
J Phys Chem B (2017) Dec 14; 121(49):11072-11084.

Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σK.
Halder S, Parrell D, Whitten D, Feig M, Kroos L.
Proc Natl Acad Sci U S A (2017) Dec 12; 114(50):E10677-E10686.

Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.
Kar P, Feig M.
J Chem Theory Comput (2017) Nov 14; 13(11):5753-5765.

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.
Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y.
J Phys Chem B (2017) Aug 31; 121(34):8009-8025.

Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane-embedded transmembrane helices.
Dutagaci B, Sayadi M, Feig M.
J Comput Chem. 2017 Jun 15;38(16):1308-1320.

Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions.
Dutagaci B, Wittayanarakul K, Mori T, Feig M.
J Chem Theory Comput (2017) Jun 13; 13(6):3049-3059.

Computational protein structure refinement: Almost there, yet still so far to go.
Feig M.
Wiley Interdiscip Rev Comput Mol Sci (2017) May-Jun; 7:(3).

Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.
Wang B, Sexton RE, Feig M.
Biochim Biophys Acta Gene Regul Mech (2017) Apr; 1860(4):482-490.

CHARMM36m: an improved force field for folded and intrinsically disordered proteins.
Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD Jr.
Nat Methods (2017) Jan; 14(1):71-73.