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Items: 1 to 50 of 76

1.

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR.

Saunders GM, Bruce Macdonald HE, Essex JW, Khalid S.

Biophys J. 2018 Oct 16;115(8):1445-1456. doi: 10.1016/j.bpj.2018.09.002. Epub 2018 Sep 13.

2.

Evaluating Anti-CD32b F(ab) Conformation Using Molecular Dynamics and Small-Angle X-Ray Scattering.

Sutton EJ, Bradshaw RT, Orr CM, Frendéus B, Larsson G, Teige I, Cragg MS, Tews I, Essex JW.

Biophys J. 2018 Jul 17;115(2):289-299. doi: 10.1016/j.bpj.2018.03.040.

3.

Unexpected finite size effects in interfacial systems: Why bigger is not always better-Increase in uncertainty of surface tension with bulk phase width.

Longford FGJ, Essex JW, Skylaris CK, Frey JG.

J Chem Phys. 2018 Jun 7;148(21):214704. doi: 10.1063/1.5025887.

PMID:
29884027
4.

Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo.

Aldeghi M, Ross GA, Bodkin MJ, Essex JW, Knapp S, Biggin PC.

Commun Chem. 2018 Apr 5;1. pii: 19. doi: 10.1038/s42004-018-0019-x.

5.

CD1b-restricted GEM T cell responses are modulated by Mycobacterium tuberculosis mycolic acid meromycolate chains.

Chancellor A, Tocheva AS, Cave-Ayland C, Tezera L, White A, Al Dulayymi JR, Bridgeman JS, Tews I, Wilson S, Lissin NM, Tebruegge M, Marshall B, Sharpe S, Elliott T, Skylaris CK, Essex JW, Baird MS, Gadola S, Elkington P, Mansour S.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):E10956-E10964. doi: 10.1073/pnas.1708252114. Epub 2017 Nov 20.

6.

Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo.

Ross GA, Bruce Macdonald HE, Cave-Ayland C, Cabedo Martinez AI, Essex JW.

J Chem Theory Comput. 2017 Dec 12;13(12):6373-6381. doi: 10.1021/acs.jctc.7b00738. Epub 2017 Nov 28.

7.

On the Calculation of Acyl Chain Order Parameters from Lipid Simulations.

Piggot TJ, Allison JR, Sessions RB, Essex JW.

J Chem Theory Comput. 2017 Nov 14;13(11):5683-5696. doi: 10.1021/acs.jctc.7b00643. Epub 2017 Oct 16.

PMID:
28876925
8.

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.

Graham JA, Essex JW, Khalid S.

J Chem Inf Model. 2017 Apr 24;57(4):650-656. doi: 10.1021/acs.jcim.7b00096. Epub 2017 Apr 4.

PMID:
28345910
9.

Conformation and Dynamics of Human Urotensin II and Urotensin Related Peptide in Aqueous Solution.

Haensele E, Mele N, Miljak M, Read CM, Whitley DC, Banting L, Delépée C, Sopkova-de Oliveira Santos J, Lepailleur A, Bureau R, Essex JW, Clark T.

J Chem Inf Model. 2017 Feb 27;57(2):298-310. doi: 10.1021/acs.jcim.6b00706. Epub 2017 Jan 23.

PMID:
28055189
10.

A Monte Carlo Resampling Approach for the Calculation of Hybrid Classical and Quantum Free Energies.

Cave-Ayland C, Skylaris CK, Essex JW.

J Chem Theory Comput. 2017 Feb 14;13(2):415-424. doi: 10.1021/acs.jctc.6b00506. Epub 2017 Jan 31.

11.

G protein coupled receptor interactions with cholesterol deep in the membrane.

Genheden S, Essex JW, Lee AG.

Biochim Biophys Acta Biomembr. 2017 Feb;1859(2):268-281. doi: 10.1016/j.bbamem.2016.12.001. Epub 2016 Dec 3.

12.

Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.

Mohamed NA, Bradshaw RT, Essex JW.

J Comput Chem. 2016 Dec 15;37(32):2749-2758. doi: 10.1002/jcc.24500. Epub 2016 Oct 19.

13.

Advanced Potential Energy Surfaces for Molecular Simulation.

Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails J, Zeng Q, Case DA, Eastman P, Wang LP, Essex JW, Head-Gordon M, Pande VS, Ponder JW, Shao Y, Skylaris CK, Todorov IT, Tuckerman ME, Head-Gordon T.

J Phys Chem B. 2016 Sep 22;120(37):9811-32. doi: 10.1021/acs.jpcb.6b06414. Review.

PMID:
27513316
14.

All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5.

Genheden S, Essex JW.

J Comput Aided Mol Des. 2016 Nov;30(11):969-976. doi: 10.1007/s10822-016-9926-z. Epub 2016 Jul 26.

15.

Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.

Bradshaw RT, Essex JW.

J Chem Theory Comput. 2016 Aug 9;12(8):3871-83. doi: 10.1021/acs.jctc.6b00276. Epub 2016 Jul 29.

16.

Reactivation of mutant p53: Constraints on mechanism highlighted by principal component analysis of the DNA binding domain.

Ouaray Z, ElSawy KM, Lane DP, Essex JW, Verma C.

Proteins. 2016 Oct;84(10):1443-61. doi: 10.1002/prot.25089. Epub 2016 Jul 26.

PMID:
27317883
17.

11th German Conference on Chemoinformatics (GCC 2015) : Fulda, Germany. 8-10 November 2015.

Fechner U, de Graaf C, Torda AE, Güssregen S, Evers A, Matter H, Hessler G, Richmond NJ, Schmidtke P, Segler MHS, Waller MP, Pleik S, Shea JE, Levine Z, Mullen R, van den Broek K, Epple M, Kuhn H, Truszkowski A, Zielesny A, Fraaije JH, Gracia RS, Kast SM, Bulusu KC, Bender A, Yosipof A, Nahum O, Senderowitz H, Krotzky T, Schulz R, Wolber G, Bietz S, Rarey M, Zimmermann MO, Lange A, Ruff M, Heidrich J, Onlia I, Exner TE, Boeckler FM, Bermudez M, Firaha DS, Hollóczki O, Kirchner B, Tautermann CS, Volkamer A, Eid S, Turk S, Rippmann F, Fulle S, Saleh N, Saladino G, Gervasio FL, Haensele E, Banting L, Whitley DC, Oliveira Santos JS, Bureau R, Clark T, Sandmann A, Lanig H, Kibies P, Heil J, Hoffgaard F, Frach R, Engel J, Smith S, Basu D, Rauh D, Kohlbacher O, Boeckler FM, Essex JW, Bodnarchuk MS, Ross GA, Finkelmann AR, Göller AH, Schneider G, Husch T, Schütter C, Balducci A, Korth M, Ntie-Kang F, Günther S, Sippl W, Mbaze LM, Ntie-Kang F, Simoben CV, Lifongo LL, Ntie-Kang F, Judson P, Barilla J, Lokajíček MV, Pisaková H, Simr P, Kireeva N, Petrov A, Ostroumov D, Solovev VP, Pervov VS, Friedrich NO, Sommer K, Rarey M, Kirchmair J, Proschak E, Weber J, Moser D, Kalinowski L, Achenbach J, Mackey M, Cheeseright T, Renner G, Renner G, Schmidt TC, Schram J, Egelkraut-Holtus M, van Oeyen A, Kalliokoski T, Fourches D, Ibezim A, Mbah CJ, Adikwu UM, Nwodo NJ, Steudle A, Masek BB, Nagy S, Baker D, Soltanshahi F, Dorfman R, Dubrucq K, Patel H, Koch O, Mrugalla F, Kast SM, Ain QU, Fuchs JE, Owen RM, Omoto K, Torella R, Pryde DC, Glen R, Bender A, Hošek P, Spiwok V, Mervin LH, Barrett I, Firth M, Murray DC, McWilliams L, Cao Q, Engkvist O, Warszycki D, Śmieja M, Bojarski AJ, Aniceto N, Freitas A, Ghafourian T, Herrmann G, Eigner-Pitto V, Naß A, Kurczab R, Bojarski AJ, Lange A, Günther MB, Hennig S, Büttner FM, Schall C, Sievers-Engler A, Ansideri F, Koch P, Stehle T, Laufer S, Böckler FM, Zdrazil B, Montanari F, Ecker GF, Grebner C, Hogner A, Ulander J, Edman K, Guallar V, Tyrchan C, Ulander J, Tyrchan C, Klute W, Bergström F, Kramer C, Nguyen QD, Frach R, Kibies P, Strohfeldt S, Böttcher S, Pongratz T, Horinek D, Kast SM, Rupp B, Al-Yamori R, Lisurek M, Kühne R, Furtado F, van den Broek K, Wessjohann L, Mathea M, Baumann K, Mohamad-Zobir SZ, Fu X, Fan TP, Bender A, Kuhn MA, Sotriffer CA, Zoufir A, Li X, Mervin L, Berg E, Polokoff M, Ihlenfeldt WD, Ihlenfeldt WD, Pretzel J, Alhalabi Z, Fraczkiewicz R, Waldman M, Clark RD, Shaikh N, Garg P, Kos A, Himmler HJ, Sandmann A, Jardin C, Sticht H, Steinbrecher TB, Dahlgren M, Cappel D, Lin T, Wang L, Krilov G, Abel R, Friesner R, Sherman W, Pöhner IA, Panecka J, Wade RC, Bietz S, Schomburg KT, Hilbig M, Rarey M, Jäger C, Wieczorek V, Westerhoff LM, Borbulevych OY, Demuth HU, Buchholz M, Schmidt D, Rickmeyer T, Krotzky T, Kolb P, Mittal S, Sánchez-García E, Nogueira MS, Oliveira TB, da Costa FB, Schmidt TJ.

J Cheminform. 2016 Apr 26;8(Suppl 1):18. doi: 10.1186/s13321-016-0119-5. No abstract available.

18.

Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells.

Mansour S, Tocheva AS, Cave-Ayland C, Machelett MM, Sander B, Lissin NM, Molloy PE, Baird MS, Stübs G, Schröder NW, Schumann RR, Rademann J, Postle AD, Jakobsen BK, Marshall BG, Gosain R, Elkington PT, Elliott T, Skylaris CK, Essex JW, Tews I, Gadola SD.

Proc Natl Acad Sci U S A. 2016 Mar 1;113(9):E1266-75. doi: 10.1073/pnas.1519246113. Epub 2016 Feb 16.

19.

A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes.

Genheden S, Essex JW.

J Chem Theory Comput. 2015 Oct 13;11(10):4749-59. doi: 10.1021/acs.jctc.5b00469. Epub 2015 Sep 8.

PMID:
26574264
20.

Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo.

Ross GA, Bodnarchuk MS, Essex JW.

J Am Chem Soc. 2015 Dec 2;137(47):14930-43. doi: 10.1021/jacs.5b07940. Epub 2015 Nov 20.

PMID:
26509924
21.

X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly.

Dinis P, Suess DL, Fox SJ, Harmer JE, Driesener RC, De La Paz L, Swartz JR, Essex JW, Britt RD, Roach PL.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1362-7. doi: 10.1073/pnas.1417252112. Epub 2015 Jan 20.

22.

A computational study of vicinal fluorination in 2,3-difluorobutane: implications for conformational control in alkane chains.

Fox SJ, Gourdain S, Coulthurst A, Fox C, Kuprov I, Essex JW, Skylaris CK, Linclau B.

Chemistry. 2015 Jan 19;21(4):1682-91. doi: 10.1002/chem.201405317. Epub 2014 Nov 21.

PMID:
25418601
23.

Direct validation of the single step classical to quantum free energy perturbation.

Cave-Ayland C, Skylaris CK, Essex JW.

J Phys Chem B. 2015 Jan 22;119(3):1017-25. doi: 10.1021/jp506459v. Epub 2014 Oct 15.

PMID:
25238649
24.

Structures of lipoyl synthase reveal a compact active site for controlling sequential sulfur insertion reactions.

Harmer JE, Hiscox MJ, Dinis PC, Fox SJ, Iliopoulos A, Hussey JE, Sandy J, Van Beek FT, Essex JW, Roach PL.

Biochem J. 2014 Nov 15;464(1):123-33. doi: 10.1042/BJ20140895.

PMID:
25100160
25.

Strategies to calculate water binding free energies in protein-ligand complexes.

Bodnarchuk MS, Viner R, Michel J, Essex JW.

J Chem Inf Model. 2014 Jun 23;54(6):1623-33. doi: 10.1021/ci400674k. Epub 2014 Jun 6.

PMID:
24684745
26.

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.

Genheden S, Cabedo Martinez AI, Criddle MP, Essex JW.

J Comput Aided Mol Des. 2014 Mar;28(3):187-200. doi: 10.1007/s10822-014-9717-3. Epub 2014 Feb 1.

PMID:
24488307
27.

Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

Fox SJ, Pittock C, Tautermann CS, Fox T, Christ C, Malcolm NO, Essex JW, Skylaris CK.

J Phys Chem B. 2013 Aug 15;117(32):9478-85. doi: 10.1021/jp404518r. Epub 2013 Aug 5.

PMID:
23841453
28.
29.

Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study.

Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS.

J Chem Inf Model. 2013 Jul 22;53(7):1700-13. doi: 10.1021/ci4001458. Epub 2013 Jun 14.

PMID:
23725291
30.

The ELBA force field for coarse-grain modeling of lipid membranes.

Orsi M, Essex JW.

PLoS One. 2011;6(12):e28637. doi: 10.1371/journal.pone.0028637. Epub 2011 Dec 16.

31.

Pocket-space maps to identify novel binding-site conformations in proteins.

Craig IR, Pfleger C, Gohlke H, Essex JW, Spiegel K.

J Chem Inf Model. 2011 Oct 24;51(10):2666-79. doi: 10.1021/ci200168b. Epub 2011 Sep 30.

PMID:
21910474
32.

Selective anticancer activity of a hexapeptide with sequence homology to a non-kinase domain of Cyclin Dependent Kinase 4.

Warenius HM, Kilburn JD, Essex JW, Maurer RI, Blaydes JP, Agarwala U, Seabra LA.

Mol Cancer. 2011 Jun 13;10:72. doi: 10.1186/1476-4598-10-72.

33.

A simple QM/MM approach for capturing polarization effects in protein-ligand binding free energy calculations.

Beierlein FR, Michel J, Essex JW.

J Phys Chem B. 2011 May 5;115(17):4911-26. doi: 10.1021/jp109054j. Epub 2011 Apr 8.

PMID:
21476567
34.

Coarse-grain modelling of DMPC and DOPC lipid bilayers.

Orsi M, Michel J, Essex JW.

J Phys Condens Matter. 2010 Apr 21;22(15):155106. doi: 10.1088/0953-8984/22/15/155106. Epub 2010 Mar 9.

PMID:
21389551
35.

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes.

Orsi M, Noro MG, Essex JW.

J R Soc Interface. 2011 Jun 6;8(59):826-41. doi: 10.1098/rsif.2010.0541. Epub 2010 Dec 3.

36.

Anisotropic elastic network modeling of entire microtubules.

Deriu MA, Soncini M, Orsi M, Patel M, Essex JW, Montevecchi FM, Redaelli A.

Biophys J. 2010 Oct 6;99(7):2190-9. doi: 10.1016/j.bpj.2010.06.070.

37.

Rigorous Free Energy Calculations in Structure-Based Drug Design.

Michel J, Foloppe N, Essex JW.

Mol Inform. 2010 Sep 17;29(8-9):570-8. doi: 10.1002/minf.201000051.

PMID:
27463452
38.

Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations.

Michel J, Essex JW.

J Comput Aided Mol Des. 2010 Aug;24(8):639-58. doi: 10.1007/s10822-010-9363-3. Epub 2010 May 28. Review.

PMID:
20509041
39.

Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments.

Craig IR, Essex JW, Spiegel K.

J Chem Inf Model. 2010 Apr 26;50(4):511-24. doi: 10.1021/ci900407c.

PMID:
20222690
40.

Permeability of small molecules through a lipid bilayer: a multiscale simulation study.

Orsi M, Sanderson WE, Essex JW.

J Phys Chem B. 2009 Sep 3;113(35):12019-29. doi: 10.1021/jp903248s.

PMID:
19663489
41.

Assessment of nonequilibrium free energy methods.

Cossins BP, Foucher S, Edge CM, Essex JW.

J Phys Chem B. 2009 Apr 23;113(16):5508-19. doi: 10.1021/jp803532z.

PMID:
19368411
42.

Conformational Motions of HIV-1 Protease Identified Using Reversible Digitally Filtered Molecular Dynamics.

Wiley AP, Williams SL, Essex JW.

J Chem Theory Comput. 2009 Apr 14;5(4):1117-28. doi: 10.1021/ct800152d.

PMID:
26609621
43.
44.

Thermal equivalence of DNA duplexes for probe design.

Weber G, Haslam N, Essex JW, Neylon C.

J Phys Condens Matter. 2009 Jan 21;21(3):034106. doi: 10.1088/0953-8984/21/3/034106. Epub 2008 Dec 17.

PMID:
21817251
45.

Protein-ligand binding affinity by nonequilibrium free energy methods.

Cossins BP, Foucher S, Edge CM, Essex JW.

J Phys Chem B. 2008 Nov 27;112(47):14985-92. doi: 10.1021/jp803533w.

PMID:
18973369
46.

Hit identification and binding mode predictions by rigorous free energy simulations.

Michel J, Essex JW.

J Med Chem. 2008 Nov 13;51(21):6654-64. doi: 10.1021/jm800524s. Epub 2008 Oct 4.

PMID:
18834104
47.

Optimal probe length varies for targets with high sequence variation: implications for probe library design for resequencing highly variable genes.

Haslam NJ, Whiteford NE, Weber G, Prügel-Bennett A, Essex JW, Neylon C.

PLoS One. 2008 Jun 18;3(6):e2500. doi: 10.1371/journal.pone.0002500.

48.

Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations.

Michel J, Orsi M, Essex JW.

J Phys Chem B. 2008 Jan 24;112(3):657-60. doi: 10.1021/jp076142y. Epub 2007 Dec 29.

PMID:
18163606
49.

A quantitative coarse-grain model for lipid bilayers.

Orsi M, Haubertin DY, Sanderson WE, Essex JW.

J Phys Chem B. 2008 Jan 24;112(3):802-15. Epub 2007 Dec 18.

PMID:
18085766
50.

Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment.

Hudson BD, Whitley DC, Ford MG, Swain M, Essex JW.

J Mol Model. 2008 Jan;14(1):49-57. Epub 2007 Nov 24.

PMID:
18038163

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