RNA–ligand molecular docking: Advances and challenges
With rapid advances in computer algorithms and hardware, fast and accurate virtual
screening has led to a drastic acceleration in selecting potent small molecules as drug …
screening has led to a drastic acceleration in selecting potent small molecules as drug …
Modern alchemical free energy methods for drug discovery explained
DM York - ACS Physical Chemistry Au, 2023 - ACS Publications
This Perspective provides a contextual explanation of the current state-of-the-art alchemical
free energy methods and their role in drug discovery as well as highlights select emerging …
free energy methods and their role in drug discovery as well as highlights select emerging …
Insights into the binding mode of AS1411 aptamer to nucleolin
AS1411 aptamer can function as a recognition probe to detect the cell surface nucleolin
overexpressed in cancer cells, however, little is known about their binding process. This …
overexpressed in cancer cells, however, little is known about their binding process. This …
Dynamics of ionic interactions at protein–nucleic acid interfaces
Conspectus Molecular association of proteins with nucleic acids is required for many
biological processes essential to life. Electrostatic interactions via ion pairs (salt bridges) of …
biological processes essential to life. Electrostatic interactions via ion pairs (salt bridges) of …
Sensitivity of the RNA structure to ion conditions as probed by molecular dynamics simulations of common canonical RNA duplexes
RNA molecules play a key role in countless biochemical processes. RNA interactions, which
are of highly diverse nature, are determined by the fact that RNA is a highly negatively …
are of highly diverse nature, are determined by the fact that RNA is a highly negatively …
Challenges and current status of computational methods for docking small molecules to nucleic acids
Since the development of the first docking program in 1982, the use of docking-based in
silico screening for potentially bioactive molecule discovery has become a common strategy …
silico screening for potentially bioactive molecule discovery has become a common strategy …
Structured waters mediate small molecule binding to G-quadruplex nucleic acids
S Neidle - Pharmaceuticals, 2021 - mdpi.com
The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-
quadruplexes can be suitable drug targets and many small molecules have been identified …
quadruplexes can be suitable drug targets and many small molecules have been identified …
Water spines and networks in G-quadruplex structures
Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop
types and orientations of individual strands, as shown by high-resolution crystal and NMR …
types and orientations of individual strands, as shown by high-resolution crystal and NMR …
Mechanism of fluoride ion encapsulation by magnesium ions in a bacterial riboswitch
Riboswitches sense various ions in bacteria and activate gene expression to synthesize
proteins that help maintain ion homeostasis. The crystal structure of the aptamer domain …
proteins that help maintain ion homeostasis. The crystal structure of the aptamer domain …
Learning to model G-quadruplexes: current methods and perspectives
I Ortiz de Luzuriaga, X Lopez… - Annual Review of …, 2021 - annualreviews.org
G-quadruplexes have raised considerable interest during the past years for the development
of therapies against cancer. These noncanonical structures of DNA may be found in …
of therapies against cancer. These noncanonical structures of DNA may be found in …