Výsledky vyhledávání

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

Autor: Solen Ekesan, Timothy Giese, Darrin York, Jinzhe Zeng

Publikováno v: Journal of Chemical Theory and Computation. 18:4304-4317

We present a fast, accurate, and robust approach for determination of free energy profiles and kinetic isotope effects for RNA 2'-O-transphosphorylation reactions with inclusion of nuclear quantum effects. We apply a deep potential range correction (

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18c8a28d9fcc79456e05972a23c791da
https://doi.org/10.1021/acs.jctc.2c00151

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

Autor: Solen Ekesan, Darrin York

Publikováno v: Organic & Biomolecular Chemistry. 20:6219-6230

Computational structural investigation (CSI) points to a new primary suspect as the general base in pistol ribozyme catalysis.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::63baa6c86f2f1ededa6ffeabd2a95a24
https://doi.org/10.1039/d2ob00234e

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AMBER Drug Discovery Boost Tools: Automated Workflow for Production Free-Energy Simulation Setup and Analysis (ProFESSA)

Autor: Darrin York, Taisung Lee, Abir Ganguly, Hsu-Chun Tsai, Mario Fernández-Pendás, Timothy Giese

Publikováno v: Journal of chemical information and modeling. 62(23)

We report an automated workflow for production free-energy simulation setup and analysis (ProFESSA) using the GPU-accelerated AMBER free-energy engine with enhanced sampling features and analysis tools, part of the AMBER Drug Discovery Boost package

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bcb101dae964ef5da4637246715c628c
https://pubmed.ncbi.nlm.nih.gov/36450130

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Multireference Generalization of the Weighted Thermodynamic Perturbation Method

Autor: Timothy Giese, Darrin York, Jinzhe Zeng

Publikováno v: The journal of physical chemistry. A. 126(45)

We describe the generalized weighted thermodynamic perturbation (gwTP) method for estimating the free energy surface of an expensive "high-level" potential energy function from the umbrella sampling performed with multiple inexpensive "low-level" ref

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::19560e583751dc8455de6c6c1a495a3f
https://pubmed.ncbi.nlm.nih.gov/36301936

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Growth of Polycyclic Aromatic Hydrocarbon and Soot Inception by in silico Simulation

Autor: Bo Wang, Jinzhe Zeng, Liqun Cao, Chih-Hao Chin, Darrin York, Tong Zhu, John Zhang

Soot is formed resulting from incomplete combustion processes of fossil fuels and is one of the most abundant specie in the space. The early stages of soot formation are central to many ongoing studies in combustion research, but its inception and gr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::98b0a98e858821dbe14c7773c2494b5b
https://doi.org/10.26434/chemrxiv-2022-qp8fc

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Modern semiempirical electronic structure methods and machine learning potentials for drug discovery: Conformers, tautomers, and protonation states

Autor: Timothy Giese, Yujun Tao, Darrin York, Jinzhe Zeng

Publikováno v: The Journal of Chemical Physics. 158:124110

Modern semiempirical electronic structure methods have considerable promise in drug discovery as universal “force fields” that can reliably model biological and drug-like molecules, including alternative tautomers and protonation states. Herein,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::3b533c7a1d0c248275e00865201be52b
https://doi.org/10.1063/5.0139281

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