Zobrazeno 1 - 4
of 4
pro vyhledávání: '"Paul B. Orndorff"'
Autor:
Paul B. Orndorff, Souvik Poddar, Aerial M. Owens, Nikita Kumari, Bryan T. Ugaz, Samrat Amin, Wade D. Van Horn, Arjan van der Vaart, Marcia Levitus
Publikováno v:
Scientific Reports, Vol 13, Iss 1, Pp 1-14 (2023)
Abstract Uracil DNA-glycosylase (UNG) is a DNA repair enzyme that removes the highly mutagenic uracil lesion from DNA using a base flipping mechanism. Although this enzyme has evolved to remove uracil from diverse sequence contexts, UNG excision effi
Externí odkaz:
https://doaj.org/article/d901f8cbb7c745719150e7b634cf7a2a
Conformational Free-Energy Differences of Large Solvated Systems with the Focused Confinement Method
Publikováno v:
Journal of Chemical Theory and Computation. 16:5163-5173
The focused confinement method (FCM) is a reaction coordinate-free simulation approach for the calculation of conformational free-energy differences in explicit solvent. The method uses reference states for the conformations of interest, partitions t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7f0c22f54f8d7bd1ac98ac8a8055141e
https://doi.org/10.1021/acs.jctc.0c00403
https://doi.org/10.1021/acs.jctc.0c00403
Autor:
Souvik Poddar, Aerial M. Pratt, Paul B. Orndorff, Arjan van der Vaart, Wade D. Van Horn, Marcia Levitus
Publikováno v:
Biophysical Journal. 122:149a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::db5cfeb7b2c3ceada6953f708778cda9
https://doi.org/10.1016/j.bpj.2022.11.1004
https://doi.org/10.1016/j.bpj.2022.11.1004
Publikováno v:
Journal of Chemical Theory and Computation. 15:6760-6768
We introduce the focused confinement method, a reaction coordinate-free simulation approach for the calculation of conformational free energies. These are obtained in a series of restrained simulations that transform part of the molecule of interest
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e31e7b564ea2611b786608b44e1931b9
https://doi.org/10.1021/acs.jctc.9b00590
https://doi.org/10.1021/acs.jctc.9b00590