Zobrazeno 1 - 10
of 207
pro vyhledávání: '"Darrin M. York"'
Autor:
Darrin M. York
Publikováno v:
ACS Physical Chemistry Au, Vol 3, Iss 6, Pp 478-491 (2023)
Externí odkaz:
https://doaj.org/article/968b35d0d5964689b7a1d39cd073c723
Publikováno v:
Molecules, Vol 29, Iss 11, p 2703 (2024)
Rare tautomeric forms of nucleobases can lead to Watson–Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guani
Externí odkaz:
https://doaj.org/article/7f2e69d09e234ee7aac28416522f80eb
Publikováno v:
ACS Omega, Vol 5, Iss 9, Pp 4611-4619 (2020)
Externí odkaz:
https://doaj.org/article/42dd42a02312406ab6a8c559b3704956
Autor:
Gerhard König, Frank C. Pickard, Jing Huang, Walter Thiel, Alexander D. MacKerell, Bernard R. Brooks, Darrin M. York
Publikováno v:
Molecules, Vol 23, Iss 10, p 2695 (2018)
Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase
Externí odkaz:
https://doaj.org/article/9b68bce499fa4e81ae79e019fa7108f5
Autor:
Erika McCarthy, Şölen Ekesan, Timothy J Giese, Timothy J Wilson, Jie Deng, Lin Huang, David M J Lilley, Darrin M York
Publikováno v:
Nucleic Acids Research. 51:4508-4518
A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classi
Autor:
Benjamin Weissman, Şölen Ekesan, Hsuan-Chun Lin, Shahbaz Gardezi, Nan-Sheng Li, Timothy J. Giese, Erika McCarthy, Michael E. Harris, Darrin M. York, Joseph A. Piccirilli
Publikováno v:
Journal of the American Chemical Society. 145:2830-2839
Autor:
Hsu-Chun Tsai, Tai-Sung Lee, Abir Ganguly, Timothy J. Giese, Maximilian CCJC Ebert, Paul Labute, Kenneth M. Merz, Darrin M. York
Publikováno v:
Journal of Chemical Theory and Computation. 19:640-658
We develop a framework for the design of optimized alchemical transformation pathways in free energy simulations using nonlinear mixing and a new functional form for so-called "softcore" potentials. We describe the implementation and testing of this
Publikováno v:
J Chem Educ
We report a new online suite of tools that enables inquiry-based active-learning activities to develop students’ representational competence about atomic orbitals. Orbital Explorer is Web site hub for the visualization and interactive investigation
Autor:
Timothy J. Giese, Darrin M. York
Publikováno v:
The Journal of Chemical Physics. 158
We use the modified Bigeleisen–Mayer equation to compute kinetic isotope effect values for non-enzymatic phosphoryl transfer reactions from classical and path integral molecular dynamics umbrella sampling. The modified form of the Bigeleisen–Maye
Publikováno v:
The Journal of Physical Chemistry B. 126:5982-5990
Electrostatic interactions are fundamental to RNA structure and function, and intimately influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic RNAs that are able to enhance reaction rates over a million-fold, despit