Docking and scoring for nucleic acid–ligand interactions: Principles and current status

Y Feng, Y Yan, J He, H Tao, Q Wu, SY Huang - Drug Discovery Today, 2022 - Elsevier
Nucleic acid (NA)–ligand interactions have crucial roles in many cellular processes and,
thus, are increasingly attracting therapeutic interest in drug discovery. Molecular docking is a …

How Good Are Current Docking Programs at Nucleic Acid–Ligand Docking? A Comprehensive Evaluation

D Jiang, H Zhao, H Du, Y Deng, Z Wu… - Journal of Chemical …, 2023 - ACS Publications
Nucleic acid (NA)–ligand interactions are of paramount importance in a variety of biological
processes, including cellular reproduction and protein biosynthesis, and therefore, NAs …

NLDock: A fast nucleic acid–ligand docking algorithm for modeling RNA/DNA–ligand complexes

Y Feng, K Zhang, Q Wu, SY Huang - Journal of Chemical …, 2021 - ACS Publications
Nucleic acid–ligand interactions play an important role in numerous cellular processes such
as gene function expression and regulation. Therefore, nucleic acids such as RNAs have …

SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity

Z Yan, J Wang - Nucleic acids research, 2017 - academic.oup.com
Nucleic acids have been widely recognized as potential targets in drug discovery and
aptamer selection. Quantifying the interactions between small molecules and nucleic acids …

ITScore-NL: an iterative knowledge-based scoring function for nucleic acid–ligand interactions

Y Feng, SY Huang - Journal of Chemical Information and …, 2020 - ACS Publications
Nucleic acid–ligand complexes underlie numerous cellular processes, such as gene
function expression and regulation, in which their three-dimensional structures are important …

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 …

NPDock: a web server for protein–nucleic acid docking

I Tuszynska, M Magnus, K Jonak… - Nucleic acids …, 2015 - academic.oup.com
Protein–RNA and protein–DNA interactions play fundamental roles in many biological
processes. A detailed understanding of these interactions requires knowledge about protein …

A nonredundant structure dataset for benchmarking protein‐RNA computational docking

SY Huang, X Zou - Journal of computational chemistry, 2013 - Wiley Online Library
Protein–RNA interactions play an important role in many biological processes. The ability to
predict the molecular structures of protein–RNA complexes from docking would be valuable …

Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein–DNA complexes

MM Gromiha, R Nagarajan - Advances in protein chemistry and structural …, 2013 - Elsevier
Protein–DNA recognition plays an important role in the regulation of gene expression.
Understanding the influence of specific residues for protein–DNA interactions and the …

[HTML][HTML] Molecular modeling applied to nucleic acid-based molecule development

A Krüger, FM Zimbres, T Kronenberger, C Wrenger - Biomolecules, 2018 - mdpi.com
Molecular modeling by means of docking and molecular dynamics (MD) has become an
integral part of early drug discovery projects, enabling the screening and enrichment of large …