Publications 1997 2018

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2018

PREFMD: A web server for protein structure refinement via molecular dynamics simulations

Heo, L. & Feig, M. Mar 15 2018 In : Bioinformatics. 34, 6, p. 1063-1065 3 p.

Research output: Contribution to journalArticle

Web Server
Protein Structure
Molecular Dynamics Simulation
Computational Biology
Molecular dynamics

Structure refinement of membrane proteins via molecular dynamics simulations

Dutagaci, B., Heo, L. & Feig, M. Jan 1 2018 (Accepted/In press) In : Proteins: Structure, Function and Bioinformatics.

Research output: Contribution to journalArticle

Water recycling
Photosensitizers
Lipid Bilayers
Molecular Dynamics Simulation
Membrane Proteins
2 Citations

What makes it difficult to refine protein models further via molecular dynamics simulations?

Heo, L. & Feig, M. Mar 1 2018 In : Proteins: Structure, Function and Bioinformatics. 86, p. 177-188 12 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Molecular dynamics
Sampling
Computer simulation
Proteins
2017
7 Citations
Protein Structure
Refinement
proteins
Proteins
sampling
9 Citations

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: Contribution to journalArticle

crowding
Computer Simulation
computerized simulation
Macromolecules
macromolecules

Determination of Hydrophobic Lengths of Membrane Proteins with the HDGB Implicit Membrane Model

Dutagaci, B. & Feig, M. Dec 26 2017 In : Journal of Chemical Information and Modeling. 57, 12, p. 3032-3042 11 p.

Research output: Contribution to journalArticle

Biological membranes
Facings
Van der Waals forces
Photosensitizers
Hydrophobicity

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: Contribution to journalArticle

scoring
decoys
discrimination
Membrane Proteins
membranes
3 Citations
Van Der Waals
Helix
Membrane
Association reactions
Membranes
4 Citations

Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields

Kar, P. & Feig, M. Nov 14 2017 In : Journal of Chemical Theory and Computation. 13, 11, p. 5753-5765 13 p.

Research output: Contribution to journalArticle

field theory (physics)
proteins
Proteins
Atoms
atoms
6 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: Contribution to journalArticle

crowding
Hydration
hydration
proteins
Proteins

Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σK

Halder, S., Parrell, D., Whitten, D., Feig, M. & Kroos, L. Dec 12 2017 In : Proceedings of the National Academy of Sciences of the United States of America. 114, 50, p. E10677-E10686

Research output: Contribution to journalArticle

Metalloproteases
Membranes
Peptide Hydrolases
Substrates
Bacilli
2 Citations

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: Contribution to journalArticle

DNA-Directed RNA Polymerases
Catalytic Domain
Nucleotides
Kinetics
Elongation
2 Citations

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

Nawrocki, G., Wang, P. H., Yu, I., Sugita, Y. & Feig, M. Dec 14 2017 In : Journal of Physical Chemistry B. 121, 49, p. 11072-11084 13 p.

Research output: Contribution to journalArticle

proteins
Proteins
crowding
field theory (physics)
Molecular dynamics
2016
32 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: Contribution to journalArticle

Cytoplasm
Metabolites
Proteins
Ligands
Cytology
74 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: Contribution to journalArticle

Intrinsically Disordered Proteins
Peptides
Molecular modeling
Proteins
Atoms
10 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: Contribution to journalArticle

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: Contribution to journalArticle

RNA
Base Pairing
sampling
Sampling
Molecular Dynamics Simulation
6 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: Contribution to journalArticle

Molecular dynamics
Proteins
simulation
Computer 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: Contribution to journalArticle

Melanocyte-Stimulating Hormones
MutS DNA Mismatch-Binding Protein
repair
Repair
adenosinetriphosphatase
11 Citations

Thermodynamics of macromolecular association in heterogeneous crowding environments: Theoretical and simulation studies with a simplified model

Ando, T., Yu, I., Feig, M. & Sugita, Y. Nov 23 2016 In : Journal of Physical Chemistry B. 120, 46, p. 11856-11865 10 p.

Research output: Contribution to journalArticle

crowding
Macromolecules
Thermodynamics
Theoretical Models
Association reactions
2015
24 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: Contribution to journalArticle

biochemistry
Biochemistry
cytoplasm
biology
Physics
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: Contribution to journalArticle

Computational methods
sampling
Sampling
membranes
Membranes
7 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: Contribution to journalArticle

DNA-Directed RNA Polymerases
Catalytic Domain
Molecular Dynamics Simulation
Catalysis
Nucleotides
30 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: Contribution to journalArticle

Molecular Dynamics Simulation
Molecular Dynamics
simulators
Molecular dynamics
Simulator
9 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: Contribution to journalArticle

amino acids
Amino acids
analogs
membranes
Membranes
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: Contribution to journalArticle

Arabidopsis
Transcription Factors
Arabidopsis thaliana
transcription factors
deterioration
12 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: Contribution to journalArticle

Enterobacter aerogenes
Urease
Nickel
Tunnels
Chemical activation
17 Citations
Molecular Dynamics Simulation
Molecular dynamics
Sampling
Computer simulation
Proteins
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: Contribution to journalArticle

Asparagine
peptides
amino acids
Amino Acids
histograms
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: Contribution to journalArticle

Retinoblastoma
Protein Stability
Proteasome Endopeptidase Complex
Tumors
Ubiquitin
2014
1 Citations
Palmitates
Phosphotransferases
Fatty Acids
Binding Sites
Ligands
9 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: Contribution to journalArticle

DNA
deoxyribonucleic acid
Sampling
sampling
simulation
8 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: Contribution to journalArticle

DNA
Nucleotides
DNA Mismatch Repair
Molecular Dynamics Simulation
Substrate Specificity
42 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: Contribution to journalArticle

Physics
Molecular Dynamics Simulation
Molecular Structure
Molecular dynamics
Trajectories
12 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: Contribution to journalArticle

Proteins
Biochemical Phenomena
Biological systems
Macromolecules
Computer Simulation
13 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: Contribution to journalArticle

Smooth Muscle Myosins
Myosin Light Chains
Phosphorylation
Light
Head
13 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: Contribution to journalArticle

environment simulation
helices
field theory (physics)
Membrane Proteins
Association reactions
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: Contribution to journalArticle

DNA-Directed RNA Polymerases
Computational methods
Nucleic Acids
Metals
Polymerization
18 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: Contribution to journalArticle

DNA
Repair
deoxyribonucleic acid
purines
pyrimidines
27 Citations
membranes
Membranes
Free energy
insertion
free energy
17 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: Contribution to journalArticle

RNA Polymerase II
Nucleosides
Molecular Dynamics Simulation
Catalysis
Eukaryota
30 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: Contribution to journalArticle

Hydration
hydration
Molecular dynamics
fragments
molecular dynamics
44 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: Contribution to journalArticle

field theory (physics)
proteins
Proteins
Molecular dynamics
molecular dynamics
43 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: Contribution to journalArticle

Molecular dynamics
molecular dynamics
proteins
Proteins
Set theory
32 Citations

Reaching new levels of realism in modeling biological macromolecules in cellular environments

Feig, M. & Sugita, Y. 2013 In : Journal of Molecular Graphics and Modelling. 45, p. 144-156 13 p.

Research output: Contribution to journalArticle

Macromolecules
macromolecules
Biomolecules
inclusions
72 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: Contribution to journalArticle

Proteins
Nuclear magnetic resonance
Cytology
Protein Stability
Molecular Dynamics Simulation
12 Citations
Phosphorylation
Sampling
Sarcoplasmic Reticulum Calcium-Transporting ATPases
phospholamban
Computer Simulation
16 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: Contribution to journalArticle

Molecular dynamics
Polarization
molecular dynamics
aqueous solutions
polarization
2012
33 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: Contribution to journalArticle

crowding
Peptides
peptides
sampling
Sampling
62 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: Contribution to journalArticle

Inclusion Bodies
Dipeptides
Proteins
Intrinsically Disordered Proteins
Protein Folding