Pesquisa | BVS Doenças Infecciosas e Parasitárias

1.

Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.

McCarthy, Erika; Ekesan, Sölen; Giese, Timothy J; Wilson, Timothy J; Deng, Jie; Huang, Lin; Lilley, David M J; York, Darrin M.

Nucleic Acids Res ; 51(9): 4508-4518, 2023 05 22.

Artigo em Inglês | MEDLINE | ID: mdl-37070188

2.

Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.

Weissman, Benjamin; Ekesan, Sölen; Lin, Hsuan-Chun; Gardezi, Shahbaz; Li, Nan-Sheng; Giese, Timothy J; McCarthy, Erika; Harris, Michael E; York, Darrin M; Piccirilli, Joseph A.

J Am Chem Soc ; 145(5): 2830-2839, 2023 02 08.

Artigo em Inglês | MEDLINE | ID: mdl-36706353

3.

Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme.

Ekesan, Sölen; York, Darrin M.

Org Biomol Chem ; 20(31): 6219-6230, 2022 08 10.

Artigo em Inglês | MEDLINE | ID: mdl-35452066

4.

Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis.

Giese, Timothy J; Ekesan, Sölen; York, Darrin M.

J Phys Chem A ; 125(19): 4216-4232, 2021 May 20.

Artigo em Inglês | MEDLINE | ID: mdl-33784093

5.

Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.

Ekesan, Sölen; York, Darrin M.

Nucleic Acids Res ; 47(19): 10282-10295, 2019 11 04.

Artigo em Inglês | MEDLINE | ID: mdl-31511899

6.

Exchange potentials for semi-classical electrons.

Herzfeld, Judith; Ekesan, Solen.

Phys Chem Chem Phys ; 18(44): 30748-30753, 2016 Nov 09.

Artigo em Inglês | MEDLINE | ID: mdl-27796385

7.

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.

Kaya, Cihan; Armutlulu, Andac; Ekesan, Solen; Haliloglu, Turkan.

Nucleic Acids Res ; 41(Web Server issue): W249-55, 2013 Jul.

Artigo em Inglês | MEDLINE | ID: mdl-23742907

8.

Transferable pseudoclassical electrons for aufbau of atomic ions.

Ekesan, Solen; Kale, Seyit; Herzfeld, Judith.

J Comput Chem ; 35(15): 1159-64, 2014 Jun 05.

Artigo em Inglês | MEDLINE | ID: mdl-24752384

9.

Surface-Accelerated String Method for Locating Minimum Free Energy Paths.

Giese, Timothy J; Ekesan, Sölen; McCarthy, Erika; Tao, Yujun; York, Darrin M.

J Chem Theory Comput ; 20(5): 2058-2073, 2024 Mar 12.

Artigo em Inglês | MEDLINE | ID: mdl-38367218

10.

Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions.

Giese, Timothy J; Zeng, Jinzhe; Ekesan, Sölen; York, Darrin M.

J Chem Theory Comput ; 18(7): 4304-4317, 2022 Jul 12.

Artigo em Inglês | MEDLINE | ID: mdl-35709391

11.

RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.

Ekesan, Sölen; McCarthy, Erika; Case, David A; York, Darrin M.

J Phys Chem B ; 126(32): 5982-5990, 2022 08 18.

Artigo em Inglês | MEDLINE | ID: mdl-35862934

12.

Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution.

Zeng, Jinzhe; Giese, Timothy J; Ekesan, Sölen; York, Darrin M.

J Chem Theory Comput ; 17(11): 6993-7009, 2021 Nov 09.

Artigo em Inglês | MEDLINE | ID: mdl-34644071

13.

Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation.

Ekesan, Sölen; York, Darrin M.

J Phys Chem B ; 123(22): 4611-4624, 2019 06 06.

Artigo em Inglês | MEDLINE | ID: mdl-31002511

14.

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes.

Bevilacqua, Philip C; Harris, Michael E; Piccirilli, Joseph A; Gaines, Colin; Ganguly, Abir; Kostenbader, Ken; Ekesan, Sölen; York, Darrin M.

ACS Chem Biol ; 14(6): 1068-1076, 2019 06 21.

Artigo em Inglês | MEDLINE | ID: mdl-31095369

15.

Magnetism and Bond Order in Diatomic Molecules Described by Semiclassical Electrons.

Ekesan, Solen; Lin, Damian Y; Herzfeld, Judith.

J Phys Chem B ; 120(26): 6264-9, 2016 07 07.

Artigo em Inglês | MEDLINE | ID: mdl-27197811

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Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.

Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.

Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme.

Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis.

Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.

Exchange potentials for semi-classical electrons.

MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues.

Transferable pseudoclassical electrons for aufbau of atomic ions.

Surface-Accelerated String Method for Locating Minimum Free Energy Paths.

Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions.

RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.

Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution.

Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation.

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes.

Magnetism and Bond Order in Diatomic Molecules Described by Semiclassical Electrons.