Ekesan Ş - Search Results

1

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials.

Tao Y, Giese TJ, Ekesan Ş, Zeng J, Aradi B, Hourahine B, Aktulga HM, Götz AW, Merz KM Jr, York DM. Tao Y, et al. Among authors: ekesan s. J Chem Phys. 2024 Jun 14;160(22):224104. doi: 10.1063/5.0211276. J Chem Phys. 2024. PMID: 38856060

2

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

Zeng J, Giese TJ, Ekesan Ş, York DM. Zeng J, et al. Among authors: ekesan s. J Chem Theory Comput. 2021 Nov 9;17(11):6993-7009. doi: 10.1021/acs.jctc.1c00201. Epub 2021 Oct 13. J Chem Theory Comput. 2021. PMID: 34644071 Free PMC article.

3

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

Giese TJ, Zeng J, Ekesan Ş, York DM. Giese TJ, et al. Among authors: ekesan s. J Chem Theory Comput. 2022 Jul 12;18(7):4304-4317. doi: 10.1021/acs.jctc.2c00151. Epub 2022 Jun 16. J Chem Theory Comput. 2022. PMID: 35709391 Free PMC article.

4

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

Giese TJ, Ekesan Ş, McCarthy E, Tao Y, York DM. Giese TJ, et al. Among authors: ekesan s. J Chem Theory Comput. 2024 Mar 12;20(5):2058-2073. doi: 10.1021/acs.jctc.3c01401. Epub 2024 Feb 17. J Chem Theory Comput. 2024. PMID: 38367218 Free PMC article.

5

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

Ekesan Ş, York DM. Ekesan Ş, et al. J Phys Chem B. 2019 Jun 6;123(22):4611-4624. doi: 10.1021/acs.jpcb.8b11923. Epub 2019 May 3. J Phys Chem B. 2019. PMID: 31002511 Free PMC article.

6

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

Ekesan Ş, York DM. Ekesan Ş, et al. Nucleic Acids Res. 2019 Nov 4;47(19):10282-10295. doi: 10.1093/nar/gkz773. Nucleic Acids Res. 2019. PMID: 31511899 Free PMC article.

7

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

Giese TJ, Ekesan Ş, York DM. Giese TJ, et al. Among authors: ekesan s. J Phys Chem A. 2021 May 20;125(19):4216-4232. doi: 10.1021/acs.jpca.1c00736. Epub 2021 Mar 30. J Phys Chem A. 2021. PMID: 33784093 Free PMC article.

8

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

Ekesan Ş, York DM. Ekesan Ş, et al. Org Biomol Chem. 2022 Aug 10;20(31):6219-6230. doi: 10.1039/d2ob00234e. Org Biomol Chem. 2022. PMID: 35452066 Free PMC article.

9

Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.

Weissman B, Ekesan Ş, Lin HC, Gardezi S, Li NS, Giese TJ, McCarthy E, Harris ME, York DM, Piccirilli JA. Weissman B, et al. Among authors: ekesan s. J Am Chem Soc. 2023 Feb 8;145(5):2830-2839. doi: 10.1021/jacs.2c10079. Epub 2023 Jan 27. J Am Chem Soc. 2023. PMID: 36706353 Free PMC article.

10

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

Ekesan Ş, McCarthy E, Case DA, York DM. Ekesan Ş, et al. J Phys Chem B. 2022 Aug 18;126(32):5982-5990. doi: 10.1021/acs.jpcb.2c03727. Epub 2022 Jul 21. J Phys Chem B. 2022. PMID: 35862934 Free PMC article.

Save citations to file

Email citations

Send citations to clipboard

Add to Collections

Add to My Bibliography

Create a file for external citation management software

Your saved search

Your RSS Feed

My Custom Filters

Publication date

Text availability

Article attribute

Article type

Article Language

Species

Sex

Age

Other

18 results

Search Page

Filters