Edina Rosta, Ph.D. - Publications

Affiliations: 
2007 Chemistry University of Southern California, Los Angeles, CA, United States 
Area:
Theoretical Chemistry and Biophysics

41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Kells A, Mihálka ZÉ, Annibale A, Rosta E. Mean first passage times in variational coarse graining using Markov state models. The Journal of Chemical Physics. 150: 134107. PMID 30954057 DOI: 10.1063/1.5083924  0.56
2018 Badaoui M, Kells A, Molteni C, Dickson CJ, Hornak V, Rosta E. Calculating Kinetic Rates and Membrane Permeability from Biased Simulation. The Journal of Physical Chemistry. B. PMID 30247032 DOI: 10.1021/acs.jpcb.8b07442  0.56
2018 Kells A, Annibale A, Rosta E. Limiting relaxation times from Markov state models. The Journal of Chemical Physics. 149: 072324. PMID 30134666 DOI: 10.1063/1.5027203  0.56
2017 Stelzl LS, Kells A, Rosta E, Hummer G. Dynamic Histogram Analysis to Determine Free Energies and Rates from Biased Simulations. Journal of Chemical Theory and Computation. PMID 29059525 DOI: 10.1021/acs.jctc.7b00373  1
2017 Leahy CT, Kells A, Hummer G, Buchete NV, Rosta E. Peptide dimerization-dissociation rates from replica exchange molecular dynamics. The Journal of Chemical Physics. 147: 152725. PMID 29055328 DOI: 10.1063/1.5004774  1
2016 Nagy GN, Suardiaz R, Lopata A, Ozohanics O, Vékey K, Brooks BR, Leveles I, Toth J, Vertessy BG, Rosta E. Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. Journal of the American Chemical Society. PMID 27740761 DOI: 10.1021/jacs.6b09012  0.36
2016 Sánchez-Sanz G, Tywoniuk B, Matallanas D, Romano D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV. SARAH Domain-Mediated MST2-RASSF Dimeric Interactions. Plos Computational Biology. 12: e1005051. PMID 27716844 DOI: 10.1371/journal.pcbi.1005051  0.76
2016 Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV. Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. The Journal of Physical Chemistry Letters. PMID 27323250 DOI: 10.1021/acs.jpclett.6b00518  1
2015 Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angewandte Chemie (International Ed. in English). PMID 26644280 DOI: 10.1002/anie.201509272  1
2015 Rosta E, Hummer G. Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model. Journal of Chemical Theory and Computation. 11: 276-85. PMID 26574225 DOI: 10.1021/ct500719p  1
2015 Sánchez-Sanz G, Matallanas D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV. MST2-RASSF protein-protein interactions through SARAH domains. Briefings in Bioinformatics. PMID 26443615 DOI: 10.1093/bib/bbv070  0.76
2015 Zheng L, Sonzini S, Ambarwati M, Rosta E, Scherman OA, Herrmann A. Turning Cucurbit[8]uril into a Supramolecular Nanoreactor for Asymmetric Catalysis. Angewandte Chemie (International Ed. in English). PMID 26383272 DOI: 10.1002/anie.201505628  1
2015 Andreou A, Leskes M, Jambrina PG, Tustin GJ, Grey CP, Rosta E, Scherman OA. Divergence from the classical hydroboration reactivity; boron containing materials through a hydroboration cascade of small cyclic dienes Chemical Science. 6: 6262-6269. DOI: 10.1039/c4sc02729a  1
2015 Lopata A, Jambrina PG, Sharma PK, Brooks BR, Toth J, Vertessy BG, Rosta E. Mutations decouple proton transfer from phosphate cleavage in the dutpase catalytic reaction Acs Catalysis. 5: 3225-3237. DOI: 10.1021/cs502087f  1
2014 Wu H, Mey AS, Rosta E, Noé F. Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states. The Journal of Chemical Physics. 141: 214106. PMID 25481128 DOI: 10.1063/1.4902240  1
2014 Bui S, von Stetten D, Jambrina PG, Prangé T, Colloc'h N, de Sanctis D, Royant A, Rosta E, Steiner RA. Direct evidence for a peroxide intermediate and a reactive enzyme-substrate-dioxygen configuration in a cofactor-free oxidase. Angewandte Chemie (International Ed. in English). 53: 13710-4. PMID 25314114 DOI: 10.1002/anie.201405485  1
2014 Jambrina PG, Bohuszewicz O, Buchete NV, Kolch W, Rosta E. Molecular mechanisms of asymmetric RAF dimer activation. Biochemical Society Transactions. 42: 784-90. PMID 25109958 DOI: 10.1042/BST20140025  1
2014 Rosta E, Yang W, Hummer G. Calcium inhibition of ribonuclease H1 two-metal ion catalysis. Journal of the American Chemical Society. 136: 3137-44. PMID 24499076 DOI: 10.1021/ja411408x  1
2014 Ganguly A, Thaplyal P, Rosta E, Bevilacqua PC, Hammes-Schiffer S. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme. Journal of the American Chemical Society. 136: 1483-96. PMID 24383543 DOI: 10.1021/ja4104217  1
2013 Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG. 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. Nucleic Acids Research. 41: 10542-55. PMID 23982515 DOI: 10.1093/nar/gkt756  1
2013 Pesnot T, Tedaldi LM, Jambrina PG, Rosta E, Wagner GK. Exploring the role of the 5-substituent for the intrinsic fluorescence of 5-aryl and 5-heteroaryl uracil nucleotides: a systematic study. Organic & Biomolecular Chemistry. 11: 6357-71. PMID 23945704 DOI: 10.1039/c3ob40485d  1
2012 Rosta E, Warshel A. On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions. Journal of Chemical Theory and Computation. 8: 3574-3585. PMID 23329895 DOI: 10.1021/ct2009329  1
2012 Lans I, Medina M, Rosta E, Hummer G, Garcia-Viloca M, Lluch JM, González-Lafont À. Theoretical study of the mechanism of the hydride transfer between ferredoxin-NADP+ reductase and NADP+: the role of Tyr303. Journal of the American Chemical Society. 134: 20544-53. PMID 23181670 DOI: 10.1021/ja310331v  1
2011 Rosta E, Nowotny M, Yang W, Hummer G. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. Journal of the American Chemical Society. 133: 8934-41. PMID 21539371 DOI: 10.1021/ja200173a  1
2010 Rosta E, Hummer G. Error and efficiency of simulated tempering simulations. The Journal of Chemical Physics. 132: 034102. PMID 20095723 DOI: 10.1063/1.3290767  1
2009 Rosta E, Buchete NV, Hummer G. Thermostat artifacts in replica exchange molecular dynamics simulations. Journal of Chemical Theory and Computation. 5: 1393-1399. PMID 20046980 DOI: 10.1021/ct800557h  1
2009 Rosta E, Hummer G. Error and efficiency of replica exchange molecular dynamics simulations. The Journal of Chemical Physics. 131: 165102. PMID 19894977 DOI: 10.1063/1.3249608  1
2009 Kamerlin SC, Cao J, Rosta E, Warshel A. On unjustifiably misrepresenting the EVB approach while simultaneously adopting it. The Journal of Physical Chemistry. B. 113: 10905-15. PMID 19606825 DOI: 10.1021/jp901709f  1
2009 Rosta E, Woodcock HL, Brooks BR, Hummer G. Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. Journal of Computational Chemistry. 30: 1634-41. PMID 19462398 DOI: 10.1002/jcc.21312  1
2008 Rosta E, Haranczyk M, Chu ZT, Warshel A. Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution. The Journal of Physical Chemistry. B. 112: 5680-92. PMID 18412414 DOI: 10.1021/jp711496y  1
2008 Rosta E, Kamerlin SC, Warshel A. On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution. Biochemistry. 47: 3725-35. PMID 18307312 DOI: 10.1021/bi702106m  1
2007 Bonaiuto J, Rosta E, Arbib M. Extending the mirror neuron system model, I: Audible actions and invisible grasps Biological Cybernetics. 96: 9-38. PMID 17028884 DOI: 10.1007/s00422-006-0110-8  1
2006 Klähn M, Rosta E, Warshel A. On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins. Journal of the American Chemical Society. 128: 15310-23. PMID 17117884 DOI: 10.1021/ja065470t  1
2006 Hong G, Rosta E, Warshel A. Using the constrained DFT approach in generating diabatic surfaces and off diagonal empirical valence bond terms for modeling reactions in condensed phases. The Journal of Physical Chemistry. B. 110: 19570-4. PMID 17004821 DOI: 10.1021/jp0625199  1
2006 Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert AT, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA, Lochan RC, Wang T, Beran GJ, Besley NA, ... ... Rosta E, et al. Advances in methods and algorithms in a modern quantum chemistry program package. Physical Chemistry Chemical Physics : Pccp. 8: 3172-91. PMID 16902710 DOI: 10.1039/b517914a  1
2006 Rosta E, Klähn M, Warshel A. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions. The Journal of Physical Chemistry. B. 110: 2934-41. PMID 16471904 DOI: 10.1021/jp057109j  1
2005 Klähn M, Braun-Sand S, Rosta E, Warshel A. On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. The Journal of Physical Chemistry. B. 109: 15645-50. PMID 16852982 DOI: 10.1021/jp0521757  1
2002 Rosta E, Surján PR. Two-body zeroth order Hamiltonians in multireference perturbation theory: The APSG reference state Journal of Chemical Physics. 116: 878-890. DOI: 10.1063/1.1427918  1
2000 Rosta E, Surjän PR. Interaction of chemical bonds. V Perturbative corrections to geminal-type wave functions International Journal of Quantum Chemistry. 80: 96-104.  1
1999 Sztáray B, Rosta E, Böcskey Z, Szepes L. Geometry and electronic structure of bis(tetrahydridoborato)bis(cyclopentadienyl)zirconium(IV) Journal of Organometallic Chemistry. 582: 267-272.  1
1999 Ángyán JG, Rosta E, Surján PR. Covalent bond orders and atomic valences from correlated wavefunctions Chemical Physics Letters. 299: 1-8.  1
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