AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
Authors
Keywords
RNA structure, Molecular structure, Drug interactions, Small molecules, Machine learning, Molecular docking, Riboswitches, Crystal structure
Journal
PLoS Computational Biology
Volume 17, Issue 2, Pages e1008309
Publisher
Public Library of Science (PLoS)
Online
2021-02-02
DOI
10.1371/journal.pcbi.1008309
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- RNAPosers: Machine Learning Classifiers for Ribonucleic Acid–Ligand Poses
- (2020) Sahil Chhabra et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Computational modeling of RNA 3D structure based on experimental data
- (2019) Almudena Ponce-Salvatierra et al. BIOSCIENCE REPORTS
- Structure–Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch
- (2018) Quentin Vicens et al. ACS Chemical Biology
- Small molecules that target group II introns are potent antifungal agents
- (2018) Olga Fedorova et al. Nature Chemical Biology
- SPA-LN: a scoring function of ligand–nucleic acid interactions via optimizing both specificity and affinity
- (2017) Zhiqiang Yan et al. NUCLEIC ACIDS RESEARCH
- Performance of machine-learning scoring functions in structure-based virtual screening
- (2017) Maciej Wójcikowski et al. Scientific Reports
- Small molecules targeting viral RNA
- (2016) Thomas Hermann Wiley Interdisciplinary Reviews-RNA
- Novel Riboswitch-Binding Flavin Analog That Protects Mice against Clostridium difficile Infection without Inhibiting Cecal Flora
- (2015) Kenneth F. Blount et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins
- (2015) Hossam M Ashtawy et al. BMC BIOINFORMATICS
- Molecular Docking and Structure-Based Drug Design Strategies
- (2015) Leonardo Ferreira et al. MOLECULES
- Selective small-molecule inhibition of an RNA structural element
- (2015) John A. Howe et al. NATURE
- SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction
- (2015) Michal J. Boniecki et al. NUCLEIC ACIDS RESEARCH
- Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field
- (2015) Maciej Wójcikowski et al. Journal of Cheminformatics
- Modeling of ribonucleic acid-ligand interactions
- (2015) Filip Stefaniak et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
- (2014) Sergio Ruiz-Carmona et al. PLoS Computational Biology
- Perspective: Coarse-grained models for biomolecular systems
- (2013) W. G. Noid JOURNAL OF CHEMICAL PHYSICS
- LigandRNA: computational predictor of RNA-ligand interactions
- (2013) A. Philips et al. RNA
- Novel Insights of Structure-Based Modeling for RNA-Targeted Drug Discovery
- (2012) Lu Chen et al. Journal of Chemical Information and Modeling
- ModeRNA server: an online tool for modeling RNA 3D structures
- (2011) M. Rother et al. BIOINFORMATICS
- RNA tertiary structure prediction with ModeRNA
- (2011) M. Rother et al. BRIEFINGS IN BIOINFORMATICS
- Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection
- (2011) Quentin Vicens et al. NUCLEIC ACIDS RESEARCH
- Open Babel: An open chemical toolbox
- (2011) Noel M O'Boyle et al. Journal of Cheminformatics
- VoteDock: Consensus docking method for prediction of protein-ligand interactions
- (2010) Dariusz Plewczynski et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression
- (2010) Elaine R. Lee et al. RNA Biology
- Using Small Molecules to Great Effect in Stem Cell Differentiation
- (2009) Kenneth S. Zaret Cell Stem Cell
- DOCK 6: Combining techniques to model RNA-small molecule complexes
- (2009) P. T. Lang et al. RNA
- Riboswitches: Emerging Themes in RNA Structure and Function
- (2008) Rebecca K. Montange et al. Annual Review of Biophysics
- Targeting RNA with Small Molecules
- (2008) Jason R. Thomas et al. CHEMICAL REVIEWS
- Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets
- (2008) Christophe Guilbert et al. Journal of Chemical Information and Modeling
- Pharao: Pharmacophore alignment and optimization
- (2008) Jonatan Taminau et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Create your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create NowBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started