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Items: 33

1.

Addendum: A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1.

Stuckey JI, Dickson BM, Cheng N, Liu Y, Norris JL, Cholensky SH, Tempel W, Qin S, Huber KG, Sagum C, Black K, Li F, Huang XP, Roth BL, Baughman BM, Senisterra G, Pattenden SG, Vedadi M, Brown PJ, TBedford M, Min J, Arrowsmith CH, James LI, Frye SV.

Nat Chem Biol. 2019 Aug;15(8):846. doi: 10.1038/s41589-019-0242-5. No abstract available.

PMID:
30842648
2.

A functional proteomics platform to reveal the sequence determinants of lysine methyltransferase substrate selectivity.

Cornett EM, Dickson BM, Krajewski K, Spellmon N, Umstead A, Vaughan RM, Shaw KM, Versluis PP, Cowles MW, Brunzelle J, Yang Z, Vega IE, Sun ZW, Rothbart SB.

Sci Adv. 2018 Nov 28;4(11):eaav2623. doi: 10.1126/sciadv.aav2623. eCollection 2018 Nov.

3.

Correction to "Quantitative Characterization of Bivalent Probes for a Dual Bromodomain Protein, Transcription Initiation Factor TFIID subunit 1".

Suh JL, Watts B, Stuckey JI, Norris-Drouin JL, Cholensky SH, Dickson BM, An Y, Mathea S, Salah E, Knapp S, Khan A, Adams AT, Strahl BD, Sagum CA, Bedford MT, James LI, Kireev DB, Frye SV.

Biochemistry. 2018 Dec 11;57(49):6806. doi: 10.1021/acs.biochem.8b01187. Epub 2018 Nov 28. No abstract available.

PMID:
30485080
4.

Erroneous Rates and False Statistical Confirmations from Infrequent Metadynamics and Other Equivalent Violations of the Hyperdynamics Paradigm.

Dickson BM.

J Chem Theory Comput. 2019 Jan 8;15(1):78-83. doi: 10.1021/acs.jctc.8b00848. Epub 2018 Dec 6.

PMID:
30468579
5.

Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies.

Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, Keogh MC, Ruthenburg AJ.

Mol Cell. 2018 Oct 4;72(1):162-177.e7. doi: 10.1016/j.molcel.2018.08.015. Epub 2018 Sep 20.

PMID:
30244833
6.

Chromatin structure and its chemical modifications regulate the ubiquitin ligase substrate selectivity of UHRF1.

Vaughan RM, Dickson BM, Whelihan MF, Johnstone AL, Cornett EM, Cheek MA, Ausherman CA, Cowles MW, Sun ZW, Rothbart SB.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):8775-8780. doi: 10.1073/pnas.1806373115. Epub 2018 Aug 13.

7.

Quantitative Characterization of Bivalent Probes for a Dual Bromodomain Protein, Transcription Initiation Factor TFIID Subunit 1.

Suh JL, Watts B, Stuckey JI, Norris-Drouin JL, Cholensky SH, Dickson BM, An Y, Mathea S, Salah E, Knapp S, Khan A, Adams AT, Strahl BD, Sagum CA, Bedford MT, James LI, Kireev DB, Frye SV.

Biochemistry. 2018 Apr 10;57(14):2140-2149. doi: 10.1021/acs.biochem.8b00150. Epub 2018 Mar 28. Erratum in: Biochemistry. 2018 Dec 11;57(49):6806.

8.

Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance.

Vaughan RM, Dickson BM, Cornett EM, Harrison JS, Kuhlman B, Rothbart SB.

Nucleic Acids Res. 2018 May 18;46(9):4405-4416. doi: 10.1093/nar/gky151.

9.

Overfill Protection and Hyperdynamics in Adaptively Biased Simulations.

Dickson BM.

J Chem Theory Comput. 2017 Dec 12;13(12):5925-5932. doi: 10.1021/acs.jctc.7b00821. Epub 2017 Nov 20.

PMID:
28974089
10.

Analysis of Histone Antibody Specificity with Peptide Microarrays.

Cornett EM, Dickson BM, Rothbart SB.

J Vis Exp. 2017 Aug 1;(126). doi: 10.3791/55912.

11.

Survey of adaptive biasing potentials: comparisons and outlook.

Dickson BM.

Curr Opin Struct Biol. 2017 Apr;43:63-67. doi: 10.1016/j.sbi.2016.11.007. Epub 2016 Nov 22. Review.

PMID:
27883951
12.

A fast, open source implementation of adaptive biasing potentials uncovers a ligand design strategy for the chromatin regulator BRD4.

Dickson BM, de Waal PW, Ramjan ZH, Xu HE, Rothbart SB.

J Chem Phys. 2016 Oct 21;145(15):154113.

13.

Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1.

Harrison JS, Cornett EM, Goldfarb D, DaRosa PA, Li ZM, Yan F, Dickson BM, Guo AH, Cantu DV, Kaustov L, Brown PJ, Arrowsmith CH, Erie DA, Major MB, Klevit RE, Krajewski K, Kuhlman B, Strahl BD, Rothbart SB.

Elife. 2016 Sep 6;5. pii: e17101. doi: 10.7554/eLife.17101.

14.

Structure-Activity Relationships and Kinetic Studies of Peptidic Antagonists of CBX Chromodomains.

Stuckey JI, Simpson C, Norris-Drouin JL, Cholensky SH, Lee J, Pasca R, Cheng N, Dickson BM, Pearce KH, Frye SV, James LI.

J Med Chem. 2016 Oct 13;59(19):8913-8923. Epub 2016 Sep 19.

15.

The structural basis of the dominant negative phenotype of the Gαi1β1γ2 G203A/A326S heterotrimer.

Liu P, Jia MZ, Zhou XE, De Waal PW, Dickson BM, Liu B, Hou L, Yin YT, Kang YY, Shi Y, Melcher K, Xu HE, Jiang Y.

Acta Pharmacol Sin. 2016 Sep;37(9):1259-72. doi: 10.1038/aps.2016.69. Epub 2016 Aug 8.

16.

ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

Dickson BM, Cornett EM, Ramjan Z, Rothbart SB.

Methods Enzymol. 2016;574:53-77. doi: 10.1016/bs.mie.2016.02.002. Epub 2016 Mar 2.

17.

Substrate Specificity Profiling of Histone-Modifying Enzymes by Peptide Microarray.

Cornett EM, Dickson BM, Vaughan RM, Krishnan S, Trievel RC, Strahl BD, Rothbart SB.

Methods Enzymol. 2016;574:31-52. doi: 10.1016/bs.mie.2016.01.008. Epub 2016 Feb 16.

18.

A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1.

Stuckey JI, Dickson BM, Cheng N, Liu Y, Norris JL, Cholensky SH, Tempel W, Qin S, Huber KG, Sagum C, Black K, Li F, Huang XP, Roth BL, Baughman BM, Senisterra G, Pattenden SG, Vedadi M, Brown PJ, Bedford MT, Min J, Arrowsmith CH, James LI, Frye SV.

Nat Chem Biol. 2016 Mar;12(3):180-7. doi: 10.1038/nchembio.2007. Epub 2016 Jan 25.

19.

μ-tempered metadynamics: Artifact independent convergence times for wide hills.

Dickson BM.

J Chem Phys. 2015 Dec 21;143(23):234109. doi: 10.1063/1.4937939.

PMID:
26696048
20.

An Interactive Database for the Assessment of Histone Antibody Specificity.

Rothbart SB, Dickson BM, Raab JR, Grzybowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenburg AJ, Strahl BD.

Mol Cell. 2015 Aug 6;59(3):502-11. doi: 10.1016/j.molcel.2015.06.022. Epub 2015 Jul 23.

21.

From histones to ribosomes: a chromatin regulator tangoes with translation.

Rothbart SB, Dickson BM, Strahl BD.

Cancer Discov. 2015 Mar;5(3):228-30. doi: 10.1158/2159-8290.CD-15-0073.

22.

Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1.

Perfetti MT, Baughman BM, Dickson BM, Mu Y, Cui G, Mader P, Dong A, Norris JL, Rothbart SB, Strahl BD, Brown PJ, Janzen WP, Arrowsmith CH, Mer G, McBride KM, James LI, Frye SV.

ACS Chem Biol. 2015 Apr 17;10(4):1072-81. doi: 10.1021/cb500956g. Epub 2015 Jan 28.

23.

High chlamydia positivity rates in Indigenous people attending Australian sexual health services.

O'Connor CC, Ali H, Guy RJ, Templeton DJ, Fairley CK, Chen MY, Dickson BM, Marshall LJ, Grulich AE, Hellard ME, Kaldor JM, Donovan B, Ward JS.

Med J Aust. 2014 Jun 2;200(10):595-8.

PMID:
24882492
24.

The structure-activity relationships of L3MBTL3 inhibitors: flexibility of the dimer interface.

Camerino MA, Zhong N, Dong A, Dickson BM, James LI, Baughman BM, Norris JL, Kireev DB, Janzen WP, Arrowsmith CH, Frye SV.

Medchemcomm. 2013 Nov;4(11):1501-1507.

25.

Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation.

Rothbart SB, Dickson BM, Ong MS, Krajewski K, Houliston S, Kireev DB, Arrowsmith CH, Strahl BD.

Genes Dev. 2013 Jun 1;27(11):1288-98. doi: 10.1101/gad.220467.113.

26.

Unrestrained computation of free energy along a path.

Dickson BM, Huang H, Post CB.

J Phys Chem B. 2012 Sep 13;116(36):11046-55. doi: 10.1021/jp304720m. Epub 2012 Aug 30.

27.

αC helix as a switch in the conformational transition of Src/CDK-like kinase domains.

Huang H, Zhao R, Dickson BM, Skeel RD, Post CB.

J Phys Chem B. 2012 Apr 19;116(15):4465-75. doi: 10.1021/jp301628r. Epub 2012 Apr 5.

28.

Approaching a parameter-free metadynamics.

Dickson BM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Sep;84(3 Pt 2):037701. Epub 2011 Sep 19.

PMID:
22060542
29.

Free energy calculations: an efficient adaptive biasing potential method.

Dickson BM, Legoll F, Lelièvre T, Stoltz G, Fleurat-Lessard P.

J Phys Chem B. 2010 May 6;114(17):5823-30. doi: 10.1021/jp100926h.

PMID:
20380408
30.

Pitfalls of choosing an order parameter for rare event calculations.

Dickson BM, Makarov DE, Henkelman G.

J Chem Phys. 2009 Aug 21;131(7):074108. doi: 10.1063/1.3204008.

PMID:
19708733
31.

Rapid sampling of reactive Langevin trajectories via noise-space Monte Carlo.

Dickson BM.

J Chem Phys. 2007 Aug 14;127(6):064106.

PMID:
17705587
32.

Parallel replica dynamics with a heterogeneous distribution of barriers: application to n-hexadecane pyrolysis.

Kum O, Dickson BM, Stuart SJ, Uberuaga BP, Voter AF.

J Chem Phys. 2004 Nov 22;121(20):9808-19.

PMID:
15549854
33.

Insulinopaenia increases 3-hydroxy-3-methylglutaryl-coenzyme A reductase levels in intestinal cells.

Moore UM, Johnson AH, Dickson BM, Tomkin GH, Collins PB.

Biochem Soc Trans. 1990 Apr;18(2):321-2. No abstract available.

PMID:
2379737

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