Publications 1997 2017

2017
3 Citations
proteins
Protein Structure
Refinement
Proteins
sampling

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Feig, M., Yu, I., Wang, P. H., Nawrocki, G. & Sugita, Y. Aug 31 2017 In : Journal of Physical Chemistry B. 121, 34, p. 8009-8025 17 p.

Research output: Research - peer-reviewArticle

crowding
computerized simulation
Computer simulation
Computer Simulation
Peptides

Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions

Dutagaci, B., Wittayanarakul, K., Mori, T. & Feig, M. Jun 13 2017 In : Journal of Chemical Theory and Computation. 13, 6, p. 3049-3059 11 p.

Research output: Research - peer-reviewArticle

scoring
discrimination
membranes
proteins
Membrane Proteins
2 Citations
Van Der Waals
Helix
Membrane
Term
Model
3 Citations

Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding

Wang, P. H., Yu, I., Feig, M. & Sugita, Y. Mar 1 2017 In : Chemical Physics Letters. 671, p. 63-70 8 p.

Research output: Research - peer-reviewArticle

crowding
hydration
proteins
Hydration
Proteins

Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity

Wang, B., Sexton, R. E. & Feig, M. Apr 1 2017 In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1860, 4, p. 482-490 9 p.

Research output: Research - peer-reviewArticle

DNA-Directed RNA Polymerases
Nucleotides
Kinetics
triphosphoric acid
Catalytic Domain
2016
16 Citations

Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

Yu, I., Mori, T., Ando, T., Harada, R., Jung, J., Sugita, Y. & Feig, M. Nov 1 2016 In : eLife. 5, NOVEMBER2016, e19274

Research output: Research - peer-reviewArticle

Cytoplasm
Proteins
Metabolites
Ligands
Molecular Models
27 Citations

CHARMM36m: An improved force field for folded and intrinsically disordered proteins

Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., De Groot, B. L., Grubmüller, H. & MacKerell, A. D. Dec 29 2016 In : Nature Methods. 14, 1, p. 71-73 3 p.

Research output: Research - peer-reviewArticle

Intrinsically Disordered Proteins
Peptides
Proteins
Molecular modeling
Atoms
5 Citations

DnaC traps DnaB as an open ring and remodels the domain that binds primase

Chodavarapu, S., Jones, A. D., Feig, M. & Kaguni, J. M. Jan 8 2016 In : Nucleic Acids Research. 44, 1, p. 210-220 11 p.

Research output: Research - peer-reviewArticle

DNA Primase
DNA Helicases
Replication Origin
Deuterium
DNA Replication
2 Citations

Intrinsic Base-Pair Rearrangement in the Hairpin Ribozyme Directs RNA Conformational Sampling and Tertiary Interface Formation

Ochieng, P. O., White, N. A., Feig, M. & Hoogstraten, C. G. Oct 27 2016 In : Journal of Physical Chemistry B. 120, 42, p. 10885-10898 14 p.

Research output: Research - peer-reviewArticle

RNA
Sampling
Catalytic RNA
hairpin ribozyme
Base Pairing
3 Citations

Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD

Feig, M. Jul 25 2016 In : Journal of Chemical Information and Modeling. 56, 7, p. 1304-1312 9 p.

Research output: Research - peer-reviewArticle

Molecular dynamics
Computer simulation
Proteins
simulation
Stereochemistry
1 Citations

Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways

Wang, B., Francis, J., Sharma, M., Law, S. M., Predeus, A. V. & Feig, M. Oct 1 2016 In : PLoS Computational Biology. 12, 10, e1005159

Research output: Research - peer-reviewArticle

Repair
Pathway
Range of data
Communication
repair
14 Citations

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms

Mori, T., Miyashita, N., Im, W., Feig, M. & Sugita, Y. Jul 1 2016 In : Biochimica et Biophysica Acta - Biomembranes. 1858, 7, p. 1635-1651 17 p.

Research output: Research - peer-reviewReview article

Biological membranes
Molecular dynamics
Membrane Proteins
Sampling
Computer simulation
2015
17 Citations

Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology

Feig, M., Harada, R., Mori, T., Yu, I., Takahashi, K. & Sugita, Y. 2015 In : Journal of Molecular Graphics and Modelling. 58, p. 1-9 9 p.

Research output: Research - peer-reviewArticle

biochemistry
cytoplasm
biology
physics
Biochemistry
8 Citations

Density-biased sampling: A robust computational method for studying pore formation in membranes

Mirjalili, V. & Feig, M. Jan 13 2015 In : Journal of Chemical Theory and Computation. 11, 1, p. 343-350 8 p.

Research output: Research - peer-reviewArticle

sampling
membranes
porosity
simulation
Computational methods
6 Citations

Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details

Wang, B., Opron, K., Burton, Z. F., Cukier, R. I. & Feig, M. Jan 30 2015 In : Nucleic Acids Research. 43, 2, p. 1133-1146 14 p.

Research output: Research - peer-reviewArticle

DNA-Directed RNA Polymerases
Catalytic Domain
Molecular Dynamics Simulation
Catalysis
Nucleotides
19 Citations

GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

Jung, J., Mori, T., Kobayashi, C., Matsunaga, Y., Yoda, T., Feig, M. & Sugita, Y. Jul 1 2015 In : Wiley Interdisciplinary Reviews: Computational Molecular Science. 5, 4, p. 310-323 14 p.

Research output: Research - peer-reviewArticle

Molecular Dynamics
Simulator
Simulation
Model
simulators
5 Citations

Interactions of amino acid side-chain analogs within membrane environments

Mirjalili, V. & Feig, M. Feb 19 2015 In : Journal of Physical Chemistry B. 119, 7, p. 2877-2885 9 p.

Research output: Research - peer-reviewArticle

amino acids
analogs
membranes
interactions
Amino acids
7 Citations

Molecular evidence for functional divergence and decay of a transcription factor derived from whole- genome duplication in Arabidopsis thaliana

Lehti-Shiu, M. D., Uygun, S., Moghe, G. D., Panchy, N., Fang, L., Hufnagel, D. E., Jasicki, H. L., Feig, M. & Shiu, S. H. Aug 1 2015 In : Plant Physiology. 168, 4, p. 1717-1734 18 p.

Research output: Research - peer-reviewArticle

Arabidopsis thaliana
transcription factors
deterioration
genome
Arabidopsis
10 Citations

Mutational and Computational Evidence That a Nickel-Transfer Tunnel in UreD Is Used for Activation of Klebsiella aerogenes Urease

Farrugia, M. A., Wang, B., Feig, M. & Hausinger, R. P. Oct 20 2015 In : Biochemistry. 54, 41, p. 6392-6401 10 p.

Research output: Research - peer-reviewArticle

Urease
Nickel
Tunnels
Chemical activation
Enterobacter aerogenes
7 Citations
Molecular dynamics
Sampling
Computer simulation
Proteins
Molecular Dynamics Simulation
1 Citations

Role of the n + 1 amino acid residue on the deamidation of asparagine in pentapeptides

Ince, H. H., Konuklar, F. A. S., Ugur, I., Ozcan, . A., Sayadi, M., Feig, M. & Aviyente, V. Dec 2 2015 In : Molecular Physics. 113, 23, p. 3839-3848 10 p.

Research output: Research - peer-reviewArticle

peptides
amino acids
water
Asparagine
Amino Acids
3 Citations

The evolutionary conserved C-terminal domains in the mammalian retinoblastoma tumor suppressor family serve as dual regulators of protein stability and transcriptional potency

Sengupta, S., Lingnurkar, R., Carey, T. S., Pomaville, M., Kar, P., Feig, M., Wilson, C. A., Knott, J. G., Arnosti, D. N. & Henry, R. W. Jun 5 2015 In : Journal of Biological Chemistry. 290, 23, p. 14462-14475 14 p.

Research output: Research - peer-reviewArticle

Proteasome Endopeptidase Complex
Tumors
Proteins
Retinoblastoma
Protein Stability
2014
1 Citations
Palmitates
Phosphotransferases
Fatty Acids
Binding Sites
Ligands
7 Citations

Conformational preferences of DNA in reduced dielectric environments

Yildirim, A., Sharma, M., Varner, B. M., Fang, L. & Feig, M. Aug 28 2014 In : Journal of Physical Chemistry B. 118, 37, p. 10874-10881 8 p.

Research output: Research - peer-reviewArticle

deoxyribonucleic acid
DNA
simulation
Sampling
sampling
5 Citations

Differential mismatch recognition specificities of eukaryotic MutS homologs, MutSα and MutSβ

Sharma, M., Predeus, A. V., Kovacs, N. & Feig, M. Jun 3 2014 In : Biophysical Journal. 106, 11, p. 2483-2492 10 p.

Research output: Research - peer-reviewArticle

DNA
Nucleotides
DNA Mismatch Repair
Molecular Dynamics Simulation
Substrate Specificity
35 Citations

Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

Mirjalili, V., Noyes, K. & Feig, M. Feb 2014 In : Proteins: Structure, Function and Bioinformatics. 82, SUPPL.2, p. 196-207 12 p.

Research output: Research - peer-reviewArticle

Molecular dynamics
Physics
Trajectories
Proteins
Molecular Dynamics Simulation
9 Citations

Recent advances in transferable coarse-grained modeling of proteins

Kar, P. & Feig, M. 2014 In : Advances in Protein Chemistry and Structural Biology. 96, p. 143-180 38 p.

Research output: Research - peer-reviewArticle

Proteins
Biological systems
Macromolecules
Atoms
Computer simulation
12 Citations

Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation

Taylor, K. A., Feig, M., Brooks, C. L., Fagnant, P. M., Lowey, S. & Trybus, K. M. Mar 2014 In : Journal of Structural Biology. 185, 3, p. 375-382 8 p.

Research output: Research - peer-reviewArticle

Smooth Muscle Myosins
Myosin Light Chains
Phosphorylation
Light
Head
10 Citations

Transferring the PRIMO coarse-grained force field to the membrane environment: Simulations of membrane proteins and helix-helix association

Kar, P., Gopal, S. M., Cheng, Y. M., Panahi, A. & Feig, M. Aug 12 2014 In : Journal of Chemical Theory and Computation. 10, 8, p. 3459-3472 14 p.

Research output: Research - peer-reviewArticle

environment simulation
helices
field theory (physics)
membranes
proteins
2013
10 Citations

Computational simulation strategies for analysis of multisubunit RNA polymerases

Wang, B., Feig, M., Cukier, R. I. & Burton, Z. F. Nov 13 2013 In : Chemical Reviews. 113, 11, p. 8546-8566 21 p.

Research output: Research - peer-reviewArticle

DNA-Directed RNA Polymerases
Computational methods
Nucleic Acids
Metals
Polymerization
16 Citations

DNA bending propensity in the presence of base mismatches: Implications for DNA repair

Sharma, M., Predeus, A. V., Mukherjee, S. & Feig, M. May 23 2013 In : Journal of Physical Chemistry B. 117, 20, p. 6194-6205 12 p.

Research output: Research - peer-reviewArticle

Repair
DNA
deoxyribonucleic acid
purine
pyrimidine
25 Citations
membranes
Membranes
insertion
free energy
Free energy
14 Citations

Energetic and structural details of the trigger-loop closing transition in RNA polymerase II

Wang, B., Predeus, A. V., Burton, Z. F. & Feig, M. Aug 6 2013 In : Biophysical Journal. 105, 3, p. 767-775 9 p.

Research output: Research - peer-reviewArticle

RNA Polymerase II
Nucleosides
triphosphoric acid
Molecular Dynamics Simulation
Catalysis
27 Citations

Interionic hydration structures of NaCl in aqueous solution: A combined study of quantum mechanical cluster calculations and QM/EFP-MD simulations

Ghosh, M. K., Re, S., Feig, M., Sugita, Y. & Choi, C. H. Jan 10 2013 In : Journal of Physical Chemistry B. 117, 1, p. 289-295 7 p.

Research output: Research - peer-reviewArticle

hydration
fragments
molecular dynamics
aqueous solutions
simulation
35 Citations

PRIMO: A transferable coarse-grained force field for proteins

Kar, P., Gopal, S. M., Cheng, Y. M., Predeus, A. & Feig, M. Aug 13 2013 In : Journal of Chemical Theory and Computation. 9, 8, p. 3769-3788 20 p.

Research output: Research - peer-reviewArticle

field theory (physics)
proteins
Proteins
molecular dynamics
atoms
32 Citations

Protein structure refinement through structure selection and averaging from molecular dynamics ensembles

Mirjalili, V. & Feig, M. Feb 12 2013 In : Journal of Chemical Theory and Computation. 9, 2, p. 1294-1303 10 p.

Research output: Research - peer-reviewArticle

molecular dynamics
proteins
Molecular dynamics
Proteins
set theory
26 Citations
Macromolecules
macromolecules
Biomolecules
inclusions
68 Citations

Reduced native state stability in crowded cellular environment due to protein-protein interactions

Harada, R., Tochio, N., Kigawa, T., Sugita, Y. & Feig, M. Mar 6 2013 In : Journal of the American Chemical Society. 135, 9, p. 3696-3701 6 p.

Research output: Research - peer-reviewArticle

Proteins
villin
Nuclear magnetic resonance
Protein Stability
Molecular Dynamics Simulation
11 Citations
Sampling
phospholamban
Phosphorylation
Sarcoplasmic Reticulum Calcium-Transporting ATPases
Switches
15 Citations

Solvent electronic polarization effects on Na+-Na+ and Cl--Cl- pair associations in aqueous solution

Choi, C. H., Re, S., Rashid, M. H. O., Li, H., Feig, M. & Sugita, Y. Aug 8 2013 In : Journal of Physical Chemistry B. 117, 31, p. 9273-9279 7 p.

Research output: Research - peer-reviewArticle

molecular dynamics
aqueous solutions
polarization
electronics
Molecular dynamics
2012
29 Citations

Conformational sampling of peptides in the presence of protein crowders from AA/CG-multiscale simulations

Predeus, A. V., Gul, S., Gopal, S. M. & Feig, M. Jul 26 2012 In : Journal of Physical Chemistry B. 116, 29, p. 8610-8620 11 p.

Research output: Research - peer-reviewArticle

crowding
peptides
sampling
proteins
simulation
50 Citations

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation

Best, R. B., Mittal, J., Feig, M. & MacKerell, A. D. Sep 5 2012 In : Biophysical Journal. 103, 5, p. 1045-1051 7 p.

Research output: Research - peer-reviewArticle

Inclusion Bodies
Proteins
alpha-Helical Protein Conformation
Dipeptides
Intrinsically Disordered Proteins
3 Citations

Molecular dynamics trajectory compression with a coarse-grained model

Cheng, Y. M., Gopal, S. M., Law, S. M. & Feig, M. 2012 In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9, 2, p. 476-486 11 p., 6051427

Research output: Research - peer-reviewArticle

Molecular Dynamics
Compression
Trajectory
Model
Data Compression
696 Citations

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ 1 and χ 2 Dihedral Angles

Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M. & MacKerell, A. D. Sep 11 2012 In : Journal of Chemical Theory and Computation. 8, 9, p. 3257-3273 17 p.

Research output: Research - peer-reviewArticle

field theory (physics)
dihedral angle
sampling
proteins
optimization
64 Citations

Protein crowding affects hydration structure and dynamics

Harada, R., Sugita, Y. & Feig, M. Mar 14 2012 In : Journal of the American Chemical Society. 134, 10, p. 4842-4849 8 p.

Research output: Research - peer-reviewArticle

Hydration
Water
Proteins
Crowding
Permittivity
21 Citations

Quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) study on intra-molecular proton transfer of glycine in water

Choi, C. H., Re, S., Feig, M. & Sugita, Y. Jun 29 2012 In : Chemical Physics Letters. 539-540, p. 218-221 4 p.

Research output: Research - peer-reviewArticle

glycine
fragments
molecular dynamics
protons
water
60 Citations
crowding
lysozyme
inhibitors
solutes
proteins
2011
12 Citations

Base-flipping mechanism in postmismatch recognition by Muts

Law, S. M. & Feig, M. 2011 In : Biophysical Journal. 101, 9, p. 2223-2231 9 p.

Research output: Research - peer-reviewArticle

DNA
DNA Mismatch Repair
Molecular Dynamics Simulation
Hydrogen Bonding
Eukaryota
4 Citations

Conformational sampling in structure prediction and refinement with atomistic and coarse-grained models

Feig, M., Gopal, S. M., Vadivel, K. & Stumpff-Kane, A. 2011 Multiscale Approaches to Protein Modeling: Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies. Springer New York, p. 85-109 25 p.

Research output: ResearchChapter

Sampling
Proteins
Atoms
Conformations