Methods to enable the design of bioactive small molecules targeting RNA
Published 2013 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Methods to enable the design of bioactive small molecules targeting RNA
Authors
Keywords
-
Journal
ORGANIC & BIOMOLECULAR CHEMISTRY
Volume 12, Issue 7, Pages 1029-1039
Publisher
Royal Society of Chemistry (RSC)
Online
2013-11-21
DOI
10.1039/c3ob42023j
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Loop-loop interaction in an adenine-sensing riboswitch: A molecular dynamics study
- (2013) O. Allner et al. RNA
- Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
- (2013) F. Di Palma et al. RNA
- Induction and reversal of myotonic dystrophy type 1 pre-mRNA splicing defects by small molecules
- (2013) Jessica L. Childs-Disney et al. Nature Communications
- The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
- (2013) Wei Huang et al. PLoS Computational Biology
- Rational Design of Bioactive, Modularly Assembled Aminoglycosides Targeting the RNA that Causes Myotonic Dystrophy Type 1
- (2012) Jessica L. Childs-Disney et al. ACS Chemical Biology
- Rationally Designed Small Molecules Targeting the RNA That Causes Myotonic Dystrophy Type 1 Are Potently Bioactive
- (2012) Jessica L. Childs-Disney et al. ACS Chemical Biology
- A Small Molecule That Targets r(CGG)exp and Improves Defects in Fragile X-Associated Tremor Ataxia Syndrome
- (2012) Matthew D. Disney et al. ACS Chemical Biology
- Chemical Correction of Pre-mRNA Splicing Defects Associated with Sequestration of Muscleblind-like 1 Protein by Expanded r(CAG)-Containing Transcripts
- (2012) Amit Kumar et al. ACS Chemical Biology
- Chemoinformatics and chemical genomics: potential utility ofin silicomethods
- (2012) Luis G. Valerio et al. JOURNAL OF APPLIED TOXICOLOGY
- Role of Ligand Binding in Structural Organization ofAddA-riboswitch Aptamer: A Molecular Dynamics Simulation
- (2012) Zhou Gong et al. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
- Identification of Small Molecule Inhibitors of the HIV-1 Nucleocapsid–Stem-Loop 3 RNA Complex
- (2012) Douglas M. Warui et al. JOURNAL OF MEDICINAL CHEMISTRY
- Molecular Mechanism of preQ1 Riboswitch Action: A Molecular Dynamics Study
- (2012) Pavel Banáš et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Design of a Bioactive Small Molecule That Targets the Myotonic Dystrophy Type 1 RNA via an RNA Motif–Ligand Database and Chemical Similarity Searching
- (2012) Raman Parkesh et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Recent Advances in Developing Small Molecules Targeting RNA
- (2011) Lirui Guan et al. ACS Chemical Biology
- Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations
- (2011) Amit Kumar et al. BIOCHEMISTRY
- NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1
- (2011) Raman Parkesh et al. BIOCHEMISTRY
- Structure–activity studies of RNA-binding oxazolidinone derivatives
- (2011) Iwona Maciagiewicz et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome
- (2011) Amit Kumar et al. CHEMBIOCHEM
- Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking
- (2011) Peter Daldrop et al. CHEMISTRY & BIOLOGY
- Small Molecule Databases and Chemical Descriptors Useful in Chemoinformatics: An Overview
- (2011) Rafael Gozalbes et al. COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
- Defining the RNA Internal Loops Preferred by Benzimidazole Derivatives via 2D Combinatorial Screening and Computational Analysis
- (2011) Sai Pradeep Velagapudi et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble
- (2011) Andrew C Stelzer et al. Nature Chemical Biology
- Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch
- (2011) U. Doshi et al. RNA
- Umbrella sampling
- (2011) Johannes Kästner Wiley Interdisciplinary Reviews-Computational Molecular Science
- Structure-Activity Relationships through Sequencing (StARTS) Defines Optimal and Suboptimal RNA Motif Targets for Small Molecules
- (2010) Sai Pradeep Velagapudi et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- RNA Dynamics by Design: Biasing Ensembles Towards the Ligand-Bound State
- (2010) Andrew C. Stelzer et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Structural Diversity of Triplet Repeat RNAs
- (2010) Krzysztof Sobczak et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Accuracy Assessment of Protein-Based Docking Programs against RNA Targets
- (2010) Yaozong Li et al. Journal of Chemical Information and Modeling
- Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine
- (2010) Ilyas Yildirim et al. Journal of Chemical Theory and Computation
- Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
- (2010) Pavel Banáš et al. Journal of Chemical Theory and Computation
- Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations
- (2010) Ron O. Dror et al. JOURNAL OF GENERAL PHYSIOLOGY
- Atomistic Details of the Ligand Discrimination Mechanism of SMK/SAM-III Riboswitch
- (2010) U. Deva Priyakumar JOURNAL OF PHYSICAL CHEMISTRY B
- Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases
- (2010) Agnieszka Kiliszek et al. NUCLEIC ACIDS RESEARCH
- Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein
- (2010) Amy Davidson et al. NUCLEIC ACIDS RESEARCH
- Rational and Modular Design of Potent Ligands Targeting the RNA That Causes Myotonic Dystrophy 2
- (2009) Melissa M. Lee et al. ACS Chemical Biology
- Search for Novel Aminoglycosides by Combining Fragment-Based Virtual Screening and 3D-QSAR Scoring
- (2009) Piotr Setny et al. Journal of Chemical Information and Modeling
- Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs
- (2009) Ilyas Yildirim et al. Journal of Chemical Theory and Computation
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- (2009) Garrett M. Morris et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Identification of Specific Small Molecule Ligands for Stem Loop 3 Ribonucleic Acid of the Packaging Signal Ψ of Human Immunodeficiency Virus-1
- (2009) Douglas M. Warui et al. JOURNAL OF MEDICINAL CHEMISTRY
- Architecture and secondary structure of an entire HIV-1 RNA genome
- (2009) Joseph M. Watts et al. NATURE
- Structural insights into CUG repeats containing the ‘stretched U–U wobble’: implications for myotonic dystrophy
- (2009) Agnieszka Kiliszek et al. NUCLEIC ACIDS RESEARCH
- Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
- (2009) A. Villa et al. NUCLEIC ACIDS RESEARCH
- A simple ligand that selectively targets CUG trinucleotide repeats and inhibits MBNL protein binding
- (2009) J. F. Arambula et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- DOCK 6: Combining techniques to model RNA-small molecule complexes
- (2009) P. T. Lang et al. RNA
- MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch
- (2009) M. Sharma et al. RNA
- Reversal of RNA Dominance by Displacement of Protein Sequestered on Triplet Repeat RNA
- (2009) T. M. Wheeler et al. SCIENCE
- Targeting RNA with Small Molecules
- (2008) Jason R. Thomas et al. CHEMICAL REVIEWS
- Anton, a special-purpose machine for molecular dynamics simulation
- (2008) David E. Shaw et al. COMMUNICATIONS OF THE ACM
- 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
- Discovery of Ligands for a Novel Target, the Human Telomerase RNA, Based on Flexible-Target Virtual Screening and NMR
- (2008) Irene Gómez Pinto et al. JOURNAL OF MEDICINAL CHEMISTRY
- 3D-QSAR and molecular docking studies of 1,3,5-triazene-2,4-diamine derivatives against r-RNA: Novel bacterial translation inhibitors
- (2008) Y. Nataraja Sekhar et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Accurate SHAPE-directed RNA structure determination
- (2008) K. E. Deigan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
- (2008) Alessandro Laio et al. REPORTS ON PROGRESS IN PHYSICS
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started