LigandRNA: computational predictor of RNA–ligand interactions

A Philips, K Milanowska, G Łach, JM Bujnicki - Rna, 2013 - rnajournal.cshlp.org
RNA molecules have recently become attractive as potential drug targets due to the
increased awareness of their importance in key biological processes. The increase of the …

RLDOCK: a new method for predicting RNA–ligand interactions

LZ Sun, Y Jiang, Y Zhou, SJ Chen - Journal of chemical theory …, 2020 - ACS Publications
The ability to accurately predict the binding site, binding pose, and binding affinity for ligand–
RNA binding is important for RNA-targeted drug design. Here, we describe a new …

RLDOCK method for predicting RNA-small molecule binding modes

Y Jiang, SJ Chen - Methods, 2022 - Elsevier
RNA molecules play critical roles in cellular functions at the level of gene expression and
regulation. The intricate 3D structures and the functional roles of RNAs make RNA …

RNA–ligand molecular docking: Advances and challenges

Y Zhou, Y Jiang, SJ Chen - Wiley Interdisciplinary Reviews …, 2022 - Wiley Online Library
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 …

DOCK 6: Combining techniques to model RNA–small molecule complexes

PT Lang, SR Brozell, S Mukherjee, EF Pettersen… - Rna, 2009 - rnajournal.cshlp.org
With an increasing interest in RNA therapeutics and for targeting RNA to treat disease, there
is a need for the tools used in protein-based drug design, particularly DOCKing algorithms …

Augmented base pairing networks encode RNA-small molecule binding preferences

C Oliver, V Mallet, RS Gendron, V Reinharz… - Nucleic acids …, 2020 - academic.oup.com
RNA-small molecule binding is a key regulatory mechanism which can stabilize 3D
structures and activate molecular functions. The discovery of RNA-targeting compounds is …

Novel insights of structure-based modeling for RNA-targeted drug discovery

L Chen, GA Calin, S Zhang - Journal of chemical information and …, 2012 - ACS Publications
Substantial progress in RNA biology highlights the importance of RNAs (eg, microRNAs) in
diseases and the potential of targeting RNAs for drug discovery. However, the lack of RNA …

DrugScoreRNAKnowledge-Based Scoring Function To Predict RNA−Ligand Interactions

P Pfeffer, H Gohlke - Journal of chemical information and …, 2007 - ACS Publications
There is growing interest in RNA as a drug target due to its widespread involvement in
biological processes. To exploit the power of structure-based drug-design approaches …

AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses

F Stefaniak, JM Bujnicki - PLoS computational biology, 2021 - journals.plos.org
RNA is considered as an attractive target for new small molecule drugs. Designing active
compounds can be facilitated by computational modeling. Most of the available tools …

Can Current Molecular Docking Methods Accurately Predict RNA Inhibitors?

KKJ Gunasinghe, IRH Ginjom, HS San… - Journal of Chemical …, 2024 - ACS Publications
Ribonucleic acids (RNAs), particularly the noncoding RNAs, play key roles in cancer,
making them attractive drug targets. While conventional methods such as high throughput …