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Items: 50

1.

Rapid metabolic shifts occur during the transition between hunger and satiety in Drosophila melanogaster.

Wilinski D, Winzeler J, Duren W, Persons JL, Holme KJ, Mosquera J, Khabiri M, Kinchen JM, Freddolino PL, Karnovsky A, Dus M.

Nat Commun. 2019 Sep 6;10(1):4052. doi: 10.1038/s41467-019-11933-z.

2.

Applications of molecular modeling to flavoproteins: Insights and challenges.

Sjulstok E, Solov'yov IA, Freddolino PL.

Methods Enzymol. 2019;620:277-314. doi: 10.1016/bs.mie.2019.03.014. Epub 2019 Apr 11.

PMID:
31072491
3.

High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster.

May CE, Vaziri A, Lin YQ, Grushko O, Khabiri M, Wang QP, Holme KJ, Pletcher SD, Freddolino PL, Neely GG, Dus M.

Cell Rep. 2019 May 7;27(6):1675-1685.e7. doi: 10.1016/j.celrep.2019.04.027.

4.

Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas.

Dolan AE, Hou Z, Xiao Y, Gramelspacher MJ, Heo J, Howden SE, Freddolino PL, Ke A, Zhang Y.

Mol Cell. 2019 Jun 6;74(5):936-950.e5. doi: 10.1016/j.molcel.2019.03.014. Epub 2019 Apr 8.

PMID:
30975459
5.

High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription.

Scholz SA, Diao R, Wolfe MB, Fivenson EM, Lin XN, Freddolino PL.

Cell Syst. 2019 Mar 27;8(3):212-225.e9. doi: 10.1016/j.cels.2019.02.004. Epub 2019 Mar 20.

PMID:
30904377
6.

Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing.

Wolfe MB, Goldstrohm AC, Freddolino PL.

Methods. 2019 Feb 15;155:88-103. doi: 10.1016/j.ymeth.2018.12.001. Epub 2018 Dec 6. Review.

PMID:
30529548
7.

Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes.

Kroner GM, Wolfe MB, Freddolino PL.

J Bacteriol. 2019 Jan 11;201(3). pii: e00411-18. doi: 10.1128/JB.00411-18. Print 2019 Feb 1.

8.

The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells.

Abshire ET, Chasseur J, Bohn JA, Del Rizzo PA, Freddolino PL, Goldstrohm AC, Trievel RC.

Nucleic Acids Res. 2018 Jul 6;46(12):6257-6270. doi: 10.1093/nar/gky412.

9.

Expression of Concern for "Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes".

Khabiri M, Freddolino PL.

J Phys Chem B. 2018 May 9. doi: 10.1021/acs.jpcb.8b04187. [Epub ahead of print] No abstract available.

PMID:
29741907
10.

Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry.

Freddolino PL, Yang J, Momen-Roknabadi A, Tavazoie S.

Elife. 2018 Apr 5;7. pii: e31867. doi: 10.7554/eLife.31867.

11.

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

Zhang C, Zheng W, Freddolino PL, Zhang Y.

J Mol Biol. 2018 Jul 20;430(15):2256-2265. doi: 10.1016/j.jmb.2018.03.004. Epub 2018 Mar 10.

12.

Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins.

Bohn JA, Van Etten JL, Schagat TL, Bowman BM, McEachin RC, Freddolino PL, Goldstrohm AC.

Nucleic Acids Res. 2018 Jan 9;46(1):362-386. doi: 10.1093/nar/gkx1120.

13.

Structure of FlgK reveals the divergence of the bacterial Hook-Filament Junction of Campylobacter.

Bulieris PV, Shaikh NH, Freddolino PL, Samatey FA.

Sci Rep. 2017 Nov 16;7(1):15743. doi: 10.1038/s41598-017-15837-0.

14.

An intrinsically disordered linker controlling the formation and the stability of the bacterial flagellar hook.

Barker CS, Meshcheryakova IV, Kostyukova AS, Freddolino PL, Samatey FA.

BMC Biol. 2017 Oct 27;15(1):97. doi: 10.1186/s12915-017-0438-7.

15.

COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information.

Zhang C, Freddolino PL, Zhang Y.

Nucleic Acids Res. 2017 Jul 3;45(W1):W291-W299. doi: 10.1093/nar/gkx366.

16.

Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes.

Khabiri M, Freddolino PL.

J Phys Chem B. 2017 May 25;121(20):5151-5161. doi: 10.1021/acs.jpcb.6b12450. Epub 2017 May 16.

17.

QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.

Ribeiro JV, Bernardi RC, Rudack T, Stone JE, Phillips JC, Freddolino PL, Schulten K.

Sci Rep. 2016 May 24;6:26536. doi: 10.1038/srep26536.

18.

Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation.

Zisis T, Freddolino PL, Turunen P, van Teeseling MC, Rowan AE, Blank KG.

Biochemistry. 2015 Sep 29;54(38):5969-79. doi: 10.1021/acs.biochem.5b00586. Epub 2015 Sep 15.

19.

Revealing the genetic basis of natural bacterial phenotypic divergence.

Freddolino PL, Goodarzi H, Tavazoie S.

J Bacteriol. 2014 Feb;196(4):825-39. doi: 10.1128/JB.01039-13. Epub 2013 Dec 6.

20.

Bacterial adaptation through loss of function.

Hottes AK, Freddolino PL, Khare A, Donnell ZN, Liu JC, Tavazoie S.

PLoS Genet. 2013;9(7):e1003617. doi: 10.1371/journal.pgen.1003617. Epub 2013 Jul 11.

21.

Signaling mechanisms of LOV domains: new insights from molecular dynamics studies.

Freddolino PL, Gardner KH, Schulten K.

Photochem Photobiol Sci. 2013 Jul;12(7):1158-70. doi: 10.1039/c3pp25400c.

22.

The dawn of virtual cell biology.

Freddolino PL, Tavazoie S.

Cell. 2012 Jul 20;150(2):248-50. doi: 10.1016/j.cell.2012.07.001.

23.

Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations.

Liu Y, Strümpfer J, Freddolino PL, Gruebele M, Schulten K.

J Phys Chem Lett. 2012 May 3;3(9):1117-1123. Epub 2012 Apr 11.

24.

Fitness landscape transformation through a single amino acid change in the rho terminator.

Freddolino PL, Goodarzi H, Tavazoie S.

PLoS Genet. 2012 May;8(5):e1002744. doi: 10.1371/journal.pgen.1002744. Epub 2012 May 31. Erratum in: PLoS Genet. 2015 Mar;11(3):e1004940.

25.

Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior.

Freddolino PL, Tavazoie S.

Annu Rev Cell Dev Biol. 2012;28:363-84. doi: 10.1146/annurev-cellbio-092910-154129. Epub 2012 May 3. Review.

PMID:
22559263
26.

Newly identified genetic variations in common Escherichia coli MG1655 stock cultures.

Freddolino PL, Amini S, Tavazoie S.

J Bacteriol. 2012 Jan;194(2):303-6. doi: 10.1128/JB.06087-11. Epub 2011 Nov 11.

27.

Stereochemical errors and their implications for molecular dynamics simulations.

Schreiner E, Trabuco LG, Freddolino PL, Schulten K.

BMC Bioinformatics. 2011 May 23;12:190. doi: 10.1186/1471-2105-12-190.

28.

Modulating LOV domain photodynamics with a residue alteration outside the chromophore binding site.

Song SH, Freddolino PL, Nash AI, Carroll EC, Schulten K, Gardner KH, Larsen DS.

Biochemistry. 2011 Apr 5;50(13):2411-23. doi: 10.1021/bi200198x. Epub 2011 Mar 1.

29.

Challenges in protein folding simulations: Timescale, representation, and analysis.

Freddolino PL, Harrison CB, Liu Y, Schulten K.

Nat Phys. 2010 Oct 1;6(10):751-758.

30.

Simulations of a protein crystal with a high resolution X-ray structure: evaluation of force fields and water models.

Cerutti DS, Freddolino PL, Duke RE Jr, Case DA.

J Phys Chem B. 2010 Oct 14;114(40):12811-24. doi: 10.1021/jp105813j.

31.

Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding.

Rajan A, Freddolino PL, Schulten K.

PLoS One. 2010 Apr 15;5(4):e9890. doi: 10.1371/journal.pone.0009890.

32.

Common structural transitions in explicit-solvent simulations of villin headpiece folding.

Freddolino PL, Schulten K.

Biophys J. 2009 Oct 21;97(8):2338-47. doi: 10.1016/j.bpj.2009.08.012.

33.

Force field bias in protein folding simulations.

Freddolino PL, Park S, Roux B, Schulten K.

Biophys J. 2009 May 6;96(9):3772-80. doi: 10.1016/j.bpj.2009.02.033.

34.

Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics.

Cerutti DS, Duke R, Freddolino PL, Fan H, Lybrand TP.

J Chem Theory Comput. 2008 Oct 14;4(10):1669-1680.

35.

Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors.

Yao Y, Harrison CB, Freddolino PL, Schulten K, Mayer ML.

EMBO J. 2008 Aug 6;27(15):2158-70. doi: 10.1038/emboj.2008.140. Epub 2008 Jul 17.

36.

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain.

Freddolino PL, Liu F, Gruebele M, Schulten K.

Biophys J. 2008 May 15;94(10):L75-7. doi: 10.1529/biophysj.108.131565. Epub 2008 Mar 13.

37.

Accelerating molecular modeling applications with graphics processors.

Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K.

J Comput Chem. 2007 Dec;28(16):2618-40.

PMID:
17894371
38.

Assembly of lipids and proteins into lipoprotein particles.

Shih AY, Arkhipov A, Freddolino PL, Sligar SG, Schulten K.

J Phys Chem B. 2007 Sep 27;111(38):11095-104. Epub 2007 Aug 14.

PMID:
17696388
39.

Disassembly of nanodiscs with cholate.

Shih AY, Freddolino PL, Sligar SG, Schulten K.

Nano Lett. 2007 Jun;7(6):1692-6. Epub 2007 May 16.

PMID:
17503871
40.

Stability and dynamics of virus capsids described by coarse-grained modeling.

Arkhipov A, Freddolino PL, Schulten K.

Structure. 2006 Dec;14(12):1767-77.

41.

Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations.

Shih AY, Freddolino PL, Arkhipov A, Schulten K.

J Struct Biol. 2007 Mar;157(3):579-92. Epub 2006 Aug 24.

PMID:
17070069
42.

Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum.

Arkhipov A, Freddolino PL, Imada K, Namba K, Schulten K.

Biophys J. 2006 Dec 15;91(12):4589-97. Epub 2006 Sep 22.

43.

Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins.

Freddolino PL, Dittrich M, Schulten K.

Biophys J. 2006 Nov 15;91(10):3630-9. Epub 2006 Aug 25. Erratum in: Biophys J. 2008 May 15;94(10):4154.

44.
45.

The role of molecular modeling in bionanotechnology.

Lu D, Aksimentiev A, Shih AY, Cruz-Chu E, Freddolino PL, Arkhipov A, Schulten K.

Phys Biol. 2006 Feb 2;3(1):S40-53. Review.

46.

Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist.

Spijker P, Vaidehi N, Freddolino PL, Hilbers PA, Goddard WA 3rd.

Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4882-7. Epub 2006 Mar 21.

47.

Molecular dynamics simulations of the complete satellite tobacco mosaic virus.

Freddolino PL, Arkhipov AS, Larson SB, McPherson A, Schulten K.

Structure. 2006 Mar;14(3):437-49.

48.

Coarse grained protein-lipid model with application to lipoprotein particles.

Shih AY, Arkhipov A, Freddolino PL, Schulten K.

J Phys Chem B. 2006 Mar 2;110(8):3674-84.

49.

The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists.

Kalani MY, Vaidehi N, Hall SE, Trabanino RJ, Freddolino PL, Kalani MA, Floriano WB, Kam VW, Goddard WA 3rd.

Proc Natl Acad Sci U S A. 2004 Mar 16;101(11):3815-20. Epub 2004 Mar 3.

50.

Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists.

Freddolino PL, Kalani MY, Vaidehi N, Floriano WB, Hall SE, Trabanino RJ, Kam VW, Goddard WA 3rd.

Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2736-41. Epub 2004 Feb 23.

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