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Items: 1 to 50 of 137

1.

Carbapenem non-susceptibility of Klebsiella pneumoniae isolates in hospitals from 2011 to 2016, data from the German Antimicrobial Resistance Surveillance (ARS).

Koppe U, von Laer A, Kroll LE, Noll I, Feig M, Schneider M, Claus H, Eckmanns T, Abu Sin M.

Antimicrob Resist Infect Control. 2018 Jun 5;7:71. doi: 10.1186/s13756-018-0362-9. eCollection 2018.

2.

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.

Jasiński M, Feig M, Trylska J.

J Chem Theory Comput. 2018 Jul 10;14(7):3603-3620. doi: 10.1021/acs.jctc.8b00291. Epub 2018 Jun 6.

PMID:
29791152
3.

Structure refinement of membrane proteins via molecular dynamics simulations.

Dutagaci B, Heo L, Feig M.

Proteins. 2018 Jul;86(7):738-750. doi: 10.1002/prot.25508. Epub 2018 May 6.

PMID:
29675899
4.

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. doi: 10.1093/nar/gky141.

5.

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. doi: 10.1073/pnas.1711467114. Epub 2017 Nov 27.

6.

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. doi: 10.1021/acs.jcim.7b00510. Epub 2017 Dec 1.

PMID:
29155578
7.

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. doi: 10.1021/acs.jpcb.7b08785. Epub 2017 Nov 30.

PMID:
29151345
8.

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

Heo L, Feig M.

Bioinformatics. 2018 Mar 15;34(6):1063-1065. doi: 10.1093/bioinformatics/btx726.

PMID:
29126101
9.

Two-gap superconductivity in Ag1-x Mo6S8 Chevrel phase.

Feig M, Bobnar M, Veremchuk I, Hennig C, Burkhardt U, Starke R, Kundys B, Leithe-Jasper A, Gumeniuk R.

J Phys Condens Matter. 2017 Dec 13;29(49):495603. doi: 10.1088/1361-648X/aa97fd.

PMID:
29099390
10.

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. doi: 10.1021/acs.jctc.7b00840. Epub 2017 Oct 19.

PMID:
28992696
11.

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. doi: 10.1002/prot.25393. Epub 2017 Oct 16.

PMID:
28975670
12.

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. doi: 10.1021/acs.jpcb.7b03570. Epub 2017 Jul 12.

13.

Assessing varicella vaccine effectiveness and its influencing factors using health insurance claims data, Germany, 2006 to 2015.

Rieck T, Feig M, An der Heiden M, Siedler A, Wichmann O.

Euro Surveill. 2017 Apr 27;22(17). pii: 30521. doi: 10.2807/1560-7917.ES.2017.22.17.30521.

14.

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. doi: 10.1021/acs.jctc.7b00254. Epub 2017 May 11.

15.

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

Wang B, Sexton RE, Feig M.

Biochim Biophys Acta. 2017 Apr;1860(4):482-490. doi: 10.1016/j.bbagrm.2017.02.008. Epub 2017 Feb 24.

17.

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. doi: 10.1002/jcc.24691. Epub 2017 Feb 4.

18.

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. doi: 10.1038/nmeth.4067. Epub 2016 Nov 7.

19.

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.

Elife. 2016 Nov 1;5. pii: e19274. doi: 10.7554/eLife.19274.

20.

Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.

Ando T, Yu I, Feig M, Sugita Y.

J Phys Chem B. 2016 Nov 23;120(46):11856-11865. Epub 2016 Nov 15.

PMID:
27797534
21.

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

Wang B, Francis J, Sharma M, Law SM, Predeus AV, Feig M.

PLoS Comput Biol. 2016 Oct 21;12(10):e1005159. doi: 10.1371/journal.pcbi.1005159. eCollection 2016 Oct.

22.

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

Ochieng PO, White NA, Feig M, Hoogstraten CG.

J Phys Chem B. 2016 Oct 5. [Epub ahead of print]

PMID:
27701852
23.

Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD.

Feig M.

J Chem Inf Model. 2016 Jul 25;56(7):1304-12. doi: 10.1021/acs.jcim.6b00222. Epub 2016 Jul 13.

24.

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

Mori T, Miyashita N, Im W, Feig M, Sugita Y.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1635-51. doi: 10.1016/j.bbamem.2015.12.032. Epub 2016 Jan 5. Review.

25.

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.

Wiley Interdiscip Rev Comput Mol Sci. 2015 Jul;5(4):310-323. Epub 2015 May 7.

26.

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

Chodavarapu S, Jones AD, Feig M, Kaguni JM.

Nucleic Acids Res. 2016 Jan 8;44(1):210-20. doi: 10.1093/nar/gkv961. Epub 2015 Sep 29.

27.

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

Farrugia MA, Wang B, Feig M, Hausinger RP.

Biochemistry. 2015 Oct 20;54(41):6392-401. doi: 10.1021/acs.biochem.5b00942. Epub 2015 Oct 5.

28.

Protein structure refinement via molecular-dynamics simulations: What works and what does not?

Feig M, Mirjalili V.

Proteins. 2016 Sep;84 Suppl 1:282-92. doi: 10.1002/prot.24871. Epub 2015 Aug 17.

29.

Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana.

Lehti-Shiu MD, Uygun S, Moghe GD, Panchy N, Fang L, Hufnagel DE, Jasicki HL, Feig M, Shiu SH.

Plant Physiol. 2015 Aug;168(4):1717-34. doi: 10.1104/pp.15.00689. Epub 2015 Jun 23.

30.

The Evolutionarily 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 TS, Pomaville M, Kar P, Feig M, Wilson CA, Knott JG, Arnosti DN, Henry RW.

J Biol Chem. 2015 Jun 5;290(23):14462-75. doi: 10.1074/jbc.M114.599993. Epub 2015 Apr 22.

31.

[MRSA and ESBL in outpatient: development from 2008 up to 2012 and socio demographic differences].

Eckmanns T, Richter D, Feig M.

Berl Munch Tierarztl Wochenschr. 2014 Sep-Oct;127(9-10):399-402. German.

PMID:
25868167
32.

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.

J Mol Graph Model. 2015 May;58:1-9. doi: 10.1016/j.jmgm.2015.02.004. Epub 2015 Feb 28.

33.

Interactions of amino acid side-chain analogs within membrane environments.

Mirjalili V, Feig M.

J Phys Chem B. 2015 Feb 19;119(7):2877-85. doi: 10.1021/jp511712u. Epub 2015 Feb 6.

34.

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

Mirjalili V, Feig M.

J Chem Theory Comput. 2015 Jan 13;11(1):343-50. doi: 10.1021/ct5009153.

35.

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

Wang B, Opron K, Burton ZF, Cukier RI, Feig M.

Nucleic Acids Res. 2015 Jan;43(2):1133-46. doi: 10.1093/nar/gku1370. Epub 2014 Dec 30.

36.

Recent advances in transferable coarse-grained modeling of proteins.

Kar P, Feig M.

Adv Protein Chem Struct Biol. 2014;96:143-80. doi: 10.1016/bs.apcsb.2014.06.005. Epub 2014 Aug 24. Review.

37.

Conformational preferences of DNA in reduced dielectric environments.

Yildirim A, Sharma M, Varner BM, Fang L, Feig M.

J Phys Chem B. 2014 Sep 18;118(37):10874-81. doi: 10.1021/jp505727w. Epub 2014 Sep 10.

38.

Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix-Helix Association.

Kar P, Gopal SM, Cheng YM, Panahi A, Feig M.

J Chem Theory Comput. 2014 Aug 12;10(8):3459-3472. Epub 2014 Jun 16.

39.

Utilization of administrative data to assess the association of an adolescent health check-up with human papillomavirus vaccine uptake in Germany.

Rieck T, Feig M, Deleré Y, Wichmann O.

Vaccine. 2014 Sep 29;32(43):5564-9. doi: 10.1016/j.vaccine.2014.07.105. Epub 2014 Aug 12.

PMID:
25131739
40.

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

Sharma M, Predeus AV, Kovacs N, Feig M.

Biophys J. 2014 Jun 3;106(11):2483-92. doi: 10.1016/j.bpj.2014.04.026.

41.

Binding site multiplicity with fatty acid ligands: implications for the regulation of PKR kinase autophosphorylation with palmitate.

Fang L, Cho HJ, Chan C, Feig M.

Proteins. 2014 Oct;82(10):2429-42. doi: 10.1002/prot.24607. Epub 2014 Jun 3.

42.

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

Taylor KA, Feig M, Brooks CL 3rd, Fagnant PM, Lowey S, Trybus KM.

J Struct Biol. 2014 Mar;185(3):375-82. doi: 10.1016/j.jsb.2013.12.008. Epub 2013 Dec 19.

43.

Vaccination coverage among children in Germany estimated by analysis of health insurance claims data.

Rieck T, Feig M, Eckmanns T, Benzler J, Siedler A, Wichmann O.

Hum Vaccin Immunother. 2014;10(2):476-84. doi: 10.4161/hv.26986. Epub 2013 Nov 5.

44.

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

Feig M, Sugita Y.

J Mol Graph Model. 2013 Sep;45:144-56. doi: 10.1016/j.jmgm.2013.08.017. Epub 2013 Aug 28. Review.

45.

PRIMO: A Transferable Coarse-grained Force Field for Proteins.

Kar P, Gopal SM, Cheng YM, Predeus A, Feig M.

J Chem Theory Comput. 2013 Aug 13;9(8):3769-3788.

46.

Computational simulation strategies for analysis of multisubunit RNA polymerases.

Wang B, Feig M, Cukier RI, Burton ZF.

Chem Rev. 2013 Nov 13;113(11):8546-66. doi: 10.1021/cr400046x. Epub 2013 Aug 29. Review. No abstract available.

47.

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

Wang B, Predeus AV, Burton ZF, Feig M.

Biophys J. 2013 Aug 6;105(3):767-75. doi: 10.1016/j.bpj.2013.05.060.

48.

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

Choi CH, Re S, Rashid MH, Li H, Feig M, Sugita Y.

J Phys Chem B. 2013 Aug 8;117(31):9273-9. doi: 10.1021/jp4049346. Epub 2013 Jul 25.

PMID:
23845041
49.

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

Mirjalili V, Noyes K, Feig M.

Proteins. 2014 Feb;82 Suppl 2:196-207. doi: 10.1002/prot.24336. Epub 2013 Aug 19.

50.

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

Sharma M, Predeus AV, Mukherjee S, Feig M.

J Phys Chem B. 2013 May 23;117(20):6194-205. doi: 10.1021/jp403127a. Epub 2013 May 10.

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