Zobrazeno 1 - 10
of 42
pro vyhledávání: '"Aaron T. Frank"'
Autor:
Jeremy Monroe, Daniel E. Eyler, Lili Mitchell, Indrajit Deb, Abigail Bojanowski, Pooja Srinivas, Christine M. Dunham, Bijoyita Roy, Aaron T. Frank, Kristin S. Koutmou
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-11 (2024)
Abstract The ribosome utilizes hydrogen bonding between mRNA codons and aminoacyl-tRNAs to ensure rapid and accurate protein production. Chemical modification of mRNA nucleobases can adjust the strength and pattern of this hydrogen bonding to alter p
Externí odkaz:
https://doaj.org/article/50975c01401849b98fd36770145e907c
Publikováno v:
Journal of Chemical Information and Modeling. 61:5589-5600
Here we report the testing and application of a simple, structure-aware framework to design target-specific screening libraries for drug development. Our approach combines advances in generative artificial intelligence (AI) with conventional molecula
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::60b29625c994e088f0efcb4315df374b
https://doi.org/10.1021/acs.jcim.1c00746
https://doi.org/10.1021/acs.jcim.1c00746
Autor:
Aaron T. Frank, Kexin Zhang
Publikováno v:
The Journal of Physical Chemistry B. 125:9970-9978
NMR-derived chemical shifts are structural fingerprints that are sensitive to the underlying conformational distributions of molecules. Thus, chemical shift data are now routinely used to infer the dynamical or conformational ensembles of peptides an
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e1bec223ebf97ea87c4e32935e0949c9
https://doi.org/10.1021/acs.jpcb.1c05651
https://doi.org/10.1021/acs.jpcb.1c05651
Publikováno v:
The Journal of Physical Chemistry B. 125:8342-8350
Estimating the binding energies of small molecules to RNA could help uncover their molecular recognition characteristics and be used to rationally design RNA-targeting chemical probes. Here, we leveraged the ability of the fragment molecular orbital
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e27310c7f7a3fa3d7bdb590eb5651fb7
https://doi.org/10.1021/acs.jpcb.1c02702
https://doi.org/10.1021/acs.jpcb.1c02702
Autor:
Jingru Xie, Aaron T. Frank
Publikováno v:
ACS Med Chem Lett
[Image: see text] Identifying potential ligand binding cavities is a critical step in structure-based screening of biomolecular targets. Cavity mapping methods can detect such binding cavities; however, for ribonucleic acid (RNA) targets, determining
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf99b6720b80abedcb6f3bd942082d1f
https://doi.org/10.1021/acsmedchemlett.1c00068
https://doi.org/10.1021/acsmedchemlett.1c00068
Autor:
Yichen Liu, Aaron T. Frank
Publikováno v:
Journal of chemical theory and computation. 18(9)
Predicting the structure (or pose) of RNA-ligand complexes is an important problem in RNA structural biology. Although one could use computational docking to rapidly sample putative poses of RNA-ligand complexes, accurately discriminating the native-
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::730c62a750cd9629969f045773b3eb8c
https://pubmed.ncbi.nlm.nih.gov/35926894
https://pubmed.ncbi.nlm.nih.gov/35926894
The ribosome relies on hydrogen bonding interactions between mRNA codons and incoming aminoacyl-tRNAs to ensure rapid and accurate protein production. The inclusion of chemically modified bases into mRNAs has the potential to alter the strength and p
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e4a26a976c76fb5b71da5b5cbd837769
https://doi.org/10.1101/2022.06.13.495988
https://doi.org/10.1101/2022.06.13.495988
Autor:
Aaron T. Frank, Jingru Xie
Publikováno v:
The Journal of Physical Chemistry B. 125:3486-3493
Riboswitches are regulatory ribonucleic acid (RNA) elements that act as ligand-dependent conformational switches that recognize their cognate ligand via a binding pocket located in their aptamer domain. In the apo form, the aptamer domain is dynamic,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::87b38cd642b5b90e72cdc9d371f22d90
https://doi.org/10.1021/acs.jpcb.0c11503
https://doi.org/10.1021/acs.jpcb.0c11503
Autor:
Ziqiao Xu, Aaron T. Frank
RNAs can recognize small-molecule ligands. However, the extent to which the molecules that they recognize differ from those recognized by proteins remains an open question. Cheminformatics analysis of experimentally validated RNA binders strongly sug
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::fb2d5d372236ae49e10dd5b636dcadb8
https://doi.org/10.1101/2022.02.05.479230
https://doi.org/10.1101/2022.02.05.479230
Autor:
Yichen Liu, Aaron T. Frank
Predicting the structure (or pose) of RNA-ligand complexes is an important problem in RNA structural biology and drug discovery. Although one could use molecular docking procedures to rapidly sample putative poses of RNA-ligand complexes, accurately
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::4e242cd1efad97751047a5724a8ed4de
https://doi.org/10.1101/2022.02.05.479229
https://doi.org/10.1101/2022.02.05.479229