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Items: 49

1.

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations.

Pan X, Rosta E, Shao Y.

Molecules. 2018 Sep 29;23(10). pii: E2500. doi: 10.3390/molecules23102500.

2.

Calculating Kinetic Rates and Membrane Permeability from Biased Simulation.

Badaoui M, Kells A, Molteni C, Dickson CJ, Hornak V, Rosta E.

J Phys Chem B. 2018 Sep 24. doi: 10.1021/acs.jpcb.8b07442. [Epub ahead of print]

PMID:
30247032
3.

Limiting relaxation times from Markov state models.

Kells A, Annibale A, Rosta E.

J Chem Phys. 2018 Aug 21;149(7):072324. doi: 10.1063/1.5027203.

PMID:
30134666
4.

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling.

Rukhlenko OS, Khorsand F, Krstic A, Rozanc J, Alexopoulos LG, Rauch N, Erickson KE, Hlavacek WS, Posner RG, Gómez-Coca S, Rosta E, Fitzgibbon C, Matallanas D, Rauch J, Kolch W, Kholodenko BN.

Cell Syst. 2018 Aug 22;7(2):161-179.e14. doi: 10.1016/j.cels.2018.06.002. Epub 2018 Jul 11.

PMID:
30007540
5.

Human DHEA sulfation requires direct interaction between PAPS synthase 2 and DHEA sulfotransferase SULT2A1.

Mueller JW, Idkowiak J, Gesteira TF, Vallet C, Hardman R, van den Boom J, Dhir V, Knauer SK, Rosta E, Arlt W.

J Biol Chem. 2018 Jun 22;293(25):9724-9735. doi: 10.1074/jbc.RA118.002248. Epub 2018 May 9.

6.

Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations.

Sharma V, Jambrina PG, Kaukonen M, Rosta E, Rich PR.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):E10339-E10348. doi: 10.1073/pnas.1708628114. Epub 2017 Nov 13.

7.

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations.

Stelzl LS, Kells A, Rosta E, Hummer G.

J Chem Theory Comput. 2017 Dec 12;13(12):6328-6342. doi: 10.1021/acs.jctc.7b00373. Epub 2017 Nov 9.

PMID:
29059525
8.

Peptide dimerization-dissociation rates from replica exchange molecular dynamics.

Leahy CT, Kells A, Hummer G, Buchete NV, Rosta E.

J Chem Phys. 2017 Oct 21;147(15):152725. doi: 10.1063/1.5004774.

PMID:
29055328
9.

Cucurbit[7]uril as a Supramolecular Artificial Enzyme for Diels-Alder Reactions.

Palma A, Artelsmair M, Wu G, Lu X, Barrow SJ, Uddin N, Rosta E, Masson E, Scherman OA.

Angew Chem Int Ed Engl. 2017 Dec 4;56(49):15688-15692. doi: 10.1002/anie.201706487. Epub 2017 Nov 3.

PMID:
29048713
10.

Smart supramolecular sensing with cucurbit[n]urils: probing hydrogen bonding with SERS.

de Nijs B, Kamp M, Szabó I, Barrow SJ, Benz F, Wu G, Carnegie C, Chikkaraddy R, Wang W, Deacon WM, Rosta E, Baumberg JJ, Scherman OA.

Faraday Discuss. 2017 Dec 4;205:505-515. doi: 10.1039/c7fd00147a.

PMID:
28932831
11.

Tracking Nanoelectrochemistry Using Individual Plasmonic Nanocavities.

Di Martino G, Turek VA, Lombardi A, Szabó I, de Nijs B, Kuhn A, Rosta E, Baumberg JJ.

Nano Lett. 2017 Aug 9;17(8):4840-4845. doi: 10.1021/acs.nanolett.7b01676. Epub 2017 Jul 17.

PMID:
28686457
12.

Modulating the oxidation of cucurbit[n]urils.

McCune JA, Rosta E, Scherman OA.

Org Biomol Chem. 2017 Jan 25;15(4):998-1005. doi: 10.1039/c6ob02594c.

PMID:
28074946
13.

A Dynamic and Responsive Host in Action: Light-Controlled Molecular Encapsulation.

Ryan ST, Del Barrio J, Suardíaz R, Ryan DF, Rosta E, Scherman OA.

Angew Chem Int Ed Engl. 2016 Dec 23;55(52):16096-16100. doi: 10.1002/anie.201607693. Epub 2016 Oct 28.

14.

Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases.

Nagy GN, Suardíaz R, Lopata A, Ozohanics O, Vékey K, Brooks BR, Leveles I, Tóth J, Vértessy BG, Rosta E.

J Am Chem Soc. 2016 Nov 16;138(45):15035-15045. Epub 2016 Nov 4.

15.

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.

Sánchez-Sanz G, Tywoniuk B, Matallanas D, Romano D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV.

PLoS Comput Biol. 2016 Oct 7;12(10):e1005051. doi: 10.1371/journal.pcbi.1005051. eCollection 2016 Oct.

16.

Turning Cucurbit[8]uril into a Supramolecular Nanoreactor for Asymmetric Catalysis.

Zheng L, Sonzini S, Ambarwati M, Rosta E, Scherman OA, Herrmann A.

Angew Chem Weinheim Bergstr Ger. 2015 Oct 26;127(44):13199-13203. Epub 2015 Sep 7.

17.

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers.

Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV.

J Phys Chem Lett. 2016 Jul 21;7(14):2676-82. doi: 10.1021/acs.jpclett.6b00518. Epub 2016 Jun 30.

PMID:
27323250
18.

Single-molecule strong coupling at room temperature in plasmonic nanocavities.

Chikkaraddy R, de Nijs B, Benz F, Barrow SJ, Scherman OA, Rosta E, Demetriadou A, Fox P, Hess O, Baumberg JJ.

Nature. 2016 Jul 7;535(7610):127-30. Epub 2016 Jun 13.

19.

Understanding the Mechanism of the Hydrogen Abstraction from Arachidonic Acid Catalyzed by the Human Enzyme 15-Lipoxygenase-2. A Quantum Mechanics/Molecular Mechanics Free Energy Simulation.

Suardíaz R, Jambrina PG, Masgrau L, González-Lafont À, Rosta E, Lluch JM.

J Chem Theory Comput. 2016 Apr 12;12(4):2079-90. doi: 10.1021/acs.jctc.5b01236. Epub 2016 Mar 9.

PMID:
26918937
20.

Light-Regulated Molecular Trafficking in a Synthetic Water-Soluble Host.

Del Barrio J, Ryan ST, Jambrina PG, Rosta E, Scherman OA.

J Am Chem Soc. 2016 May 11;138(18):5745-8. doi: 10.1021/jacs.5b11642. Epub 2016 Apr 28.

PMID:
26876686
21.

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation.

Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E.

Angew Chem Int Ed Engl. 2016 Jan 18;55(3):983-6. doi: 10.1002/anie.201509272. Epub 2015 Dec 8.

22.

Free energies from dynamic weighted histogram analysis using unbiased Markov state model.

Rosta E, Hummer G.

J Chem Theory Comput. 2015 Jan 13;11(1):276-85. doi: 10.1021/ct500719p. Epub 2014 Dec 23.

PMID:
26574225
23.

Divergence from the classical hydroboration reactivity; boron containing materials through a hydroboration cascade of small cyclic dienes.

Andreou A, Leskes M, Jambrina PG, Tustin GJ, Grey CP, Rosta E, Scherman OA.

Chem Sci. 2015 Nov 1;6(11):6262-6269. doi: 10.1039/c4sc02729a. Epub 2015 Aug 6.

24.

MST2-RASSF protein-protein interactions through SARAH domains.

Sánchez-Sanz G, Matallanas D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV.

Brief Bioinform. 2016 Jul;17(4):593-602. doi: 10.1093/bib/bbv070. Epub 2015 Oct 5.

25.

Turning Cucurbit[8]uril into a Supramolecular Nanoreactor for Asymmetric Catalysis.

Zheng L, Sonzini S, Ambarwati M, Rosta E, Scherman OA, Herrmann A.

Angew Chem Int Ed Engl. 2015 Oct 26;54(44):13007-11. doi: 10.1002/anie.201505628. Epub 2015 Sep 7.

26.

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states.

Wu H, Mey AS, Rosta E, Noé F.

J Chem Phys. 2014 Dec 7;141(21):214106. doi: 10.1063/1.4902240.

PMID:
25481128
27.

Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase.

Bui S, von Stetten D, Jambrina PG, Prangé T, Colloc'h N, de Sanctis D, Royant A, Rosta E, Steiner RA.

Angew Chem Int Ed Engl. 2014 Dec 8;53(50):13710-4. doi: 10.1002/anie.201405485. Epub 2014 Oct 14.

28.

Molecular mechanisms of asymmetric RAF dimer activation.

Jambrina PG, Bohuszewicz O, Buchete NV, Kolch W, Rosta E.

Biochem Soc Trans. 2014 Aug;42(4):784-90. doi: 10.1042/BST20140025. Review.

PMID:
25109958
29.

Calcium inhibition of ribonuclease H1 two-metal ion catalysis.

Rosta E, Yang W, Hummer G.

J Am Chem Soc. 2014 Feb 26;136(8):3137-44. doi: 10.1021/ja411408x. Epub 2014 Feb 18.

30.

Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme.

Ganguly A, Thaplyal P, Rosta E, Bevilacqua PC, Hammes-Schiffer S.

J Am Chem Soc. 2014 Jan 29;136(4):1483-96. doi: 10.1021/ja4104217. Epub 2014 Jan 15.

31.

Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.

Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG.

Nucleic Acids Res. 2013 Dec;41(22):10542-55. doi: 10.1093/nar/gkt756. Epub 2013 Aug 27.

32.

Exploring the role of the 5-substituent for the intrinsic fluorescence of 5-aryl and 5-heteroaryl uracil nucleotides: a systematic study.

Pesnot T, Tedaldi LM, Jambrina PG, Rosta E, Wagner GK.

Org Biomol Chem. 2013 Oct 7;11(37):6357-71. doi: 10.1039/c3ob40485d.

PMID:
23945704
33.
34.

Theoretical study of the mechanism of the hydride transfer between ferredoxin-NADP+ reductase and NADP+: the role of Tyr303.

Lans I, Medina M, Rosta E, Hummer G, Garcia-Viloca M, Lluch JM, González-Lafont À.

J Am Chem Soc. 2012 Dec 19;134(50):20544-53. doi: 10.1021/ja310331v. Epub 2012 Dec 10.

PMID:
23181670
35.

[Health behavior of medical students. Introduction of mental hygienic skills in the medical education in Hungary].

Rosta E, Almási Z, Karácsony I, Konkolÿ Thege B, Hegedűs K.

Orv Hetil. 2012 Jul 22;153(29):1153-7. doi: 10.1556/OH.2012.29374. Hungarian.

PMID:
22805041
36.

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.

Rosta E, Nowotny M, Yang W, Hummer G.

J Am Chem Soc. 2011 Jun 15;133(23):8934-41. doi: 10.1021/ja200173a. Epub 2011 May 24.

37.

Error and efficiency of simulated tempering simulations.

Rosta E, Hummer G.

J Chem Phys. 2010 Jan 21;132(3):034102. doi: 10.1063/1.3290767.

38.

Thermostat artifacts in replica exchange molecular dynamics simulations.

Rosta E, Buchete NV, Hummer G.

J Chem Theory Comput. 2009;5(5):1393-1399.

39.

Error and efficiency of replica exchange molecular dynamics simulations.

Rosta E, Hummer G.

J Chem Phys. 2009 Oct 28;131(16):165102. doi: 10.1063/1.3249608.

40.

On unjustifiably misrepresenting the EVB approach while simultaneously adopting it.

Kamerlin SC, Cao J, Rosta E, Warshel A.

J Phys Chem B. 2009 Aug 6;113(31):10905-15. doi: 10.1021/jp901709f.

41.

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

Rosta E, Woodcock HL, Brooks BR, Hummer G.

J Comput Chem. 2009 Aug;30(11):1634-41. doi: 10.1002/jcc.21312.

42.

Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

Rosta E, Haranczyk M, Chu ZT, Warshel A.

J Phys Chem B. 2008 May 8;112(18):5680-92. doi: 10.1021/jp711496y. Epub 2008 Apr 16.

43.

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution.

Rosta E, Kamerlin SC, Warshel A.

Biochemistry. 2008 Mar 25;47(12):3725-35. doi: 10.1021/bi702106m. Epub 2008 Feb 29.

PMID:
18307312
44.

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins.

Klähn M, Rosta E, Warshel A.

J Am Chem Soc. 2006 Nov 29;128(47):15310-23.

PMID:
17117884
45.

Extending the mirror neuron system model, I. Audible actions and invisible grasps.

Bonaiuto J, Rosta E, Arbib M.

Biol Cybern. 2007 Jan;96(1):9-38. Epub 2006 Oct 7.

PMID:
17028884
47.

Advances in methods and algorithms in a modern quantum chemistry program package.

Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert AT, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA Jr, Lochan RC, Wang T, Beran GJ, Besley NA, Herbert JM, Lin CY, Van Voorhis T, Chien SH, Sodt A, Steele RP, Rassolov VA, Maslen PE, Korambath PP, Adamson RD, Austin B, Baker J, Byrd EF, Dachsel H, Doerksen RJ, Dreuw A, Dunietz BD, Dutoi AD, Furlani TR, Gwaltney SR, Heyden A, Hirata S, Hsu CP, Kedziora G, Khalliulin RZ, Klunzinger P, Lee AM, Lee MS, Liang W, Lotan I, Nair N, Peters B, Proynov EI, Pieniazek PA, Rhee YM, Ritchie J, Rosta E, Sherrill CD, Simmonett AC, Subotnik JE, Woodcock HL 3rd, Zhang W, Bell AT, Chakraborty AK, Chipman DM, Keil FJ, Warshel A, Hehre WJ, Schaefer HF 3rd, Kong J, Krylov AI, Gill PM, Head-Gordon M.

Phys Chem Chem Phys. 2006 Jul 21;8(27):3172-91. Epub 2006 Jun 12. Review.

PMID:
16902710
48.
49.

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.

Rosta E, Klähn M, Warshel A.

J Phys Chem B. 2006 Feb 16;110(6):2934-41.

PMID:
16471904

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