Zobrazeno 1 - 10
of 118
pro vyhledávání: '"Ioan Andricioaei"'
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-10 (2018)
DNA is found in a dynamic equilibrium between standard Watson-Crick (WC) base pairs and non-standard Hoogsteen (HG) base pairs. Here the authors describe the influence of echinomycin and actinomycin D ligands binding on the HG-WC base pair dynamics i
Externí odkaz:
https://doaj.org/article/b13b41ea233f4bdb8b17d86942bc33d6
Publikováno v:
Journal of Chemical Information and Modeling. 62:6749-6761
The Hoogsteen (HG) base pairing conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in previous studi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::66a0bdc0fedad9ebfbd2c90d6e0ef902
https://doi.org/10.1021/acs.jcim.2c00519
https://doi.org/10.1021/acs.jcim.2c00519
Autor:
Anthony T. Bogetti, Jeremy M. G. Leung, John D. Russo, She Zhang, Jeff P. Thompson, Ali S. Saglam, Dhiman Ray, Rhea C. Abraham, James R. Faeder, Ioan Andricioaei, Joshua L. Adelman, Matthew C. Zwier, David N. LeBard, Daniel M. Zuckerman, Lillian T. Chong
We present six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for enabling applications of the weighted ensemble (WE) pa
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c5823b98c7575c47bf7d377a5187b9db
https://doi.org/10.1101/2022.10.04.510803
https://doi.org/10.1101/2022.10.04.510803
Publikováno v:
The Journal of Chemical Physics. 158:134108
Allostery in proteins involves, broadly speaking, ligand-induced conformational transitions that modulate function at active sites distal to where the ligand binds. In contrast, the concept of cooperativity (in the sense used in phase transition theo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::795cca3c989d0cd53b747a86663f717d
https://doi.org/10.1063/5.0140113
https://doi.org/10.1063/5.0140113
Publikováno v:
Biophysical Journal. 122:423a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f17e3d0525d1b130e40df6955d5525d1
https://doi.org/10.1016/j.bpj.2022.11.2294
https://doi.org/10.1016/j.bpj.2022.11.2294
We introduce a rare-event sampling scheme, named Markovian Weighted Ensemble Milestoning (M-WEM), which inlays a weighted ensemble framework within a Markovian milestoning theory to efficiently calculate thermodynamic and kinetic properties of long-t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::20e9aa0c59670db1064bd4aa6c250b9d
https://doi.org/10.1101/2021.06.26.450057
https://doi.org/10.1101/2021.06.26.450057
Publikováno v:
Proc Natl Acad Sci U S A
The virus bacteriophage T4, from the family Myoviridae, employs an intriguing contractile injection machine to inject its genome into the bacterium Escherichia coli. Although the atomic structure of phage T4 is largely understood, the dynamics of its
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0c609517d42d50bf50c85f2ba75778d0
https://doi.org/10.1073/pnas.1909298116
https://doi.org/10.1073/pnas.1909298116
Publikováno v:
The Journal of chemical physics. 153(15)
We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociation dynamics. We performed WEM simulations on the following host-guest s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d09c6f9906efa46a8961e6ea3be675f6
https://pubmed.ncbi.nlm.nih.gov/33092382
https://pubmed.ncbi.nlm.nih.gov/33092382
Autor:
Ioan Andricioaei, Dhiman Ray
Genetic information is encoded in the DNA double helix which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleobase pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogstee
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::640543d640eb9ed7af8486ac31f9b1db
Publikováno v:
TheScienceBreaker.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::050bb6ba1bc8b53272d98cc926fb36d5
https://doi.org/10.25250/thescbr.brk395
https://doi.org/10.25250/thescbr.brk395