High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble

Non-coding RNAs as drug targets

(2016) Masayuki Matsui et al.   NATURE REVIEWS DRUG DISCOVERY

Small molecules targeting viral RNA

(2016) Thomas Hermann   Wiley Interdisciplinary Reviews-RNA

Structure based approaches for targeting non-coding RNAs with small molecules

(2015) Matthew D Shortridge et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

FlexAID: Revisiting Docking on Non-Native-Complex Structures

(2015) Francis Gaudreault et al.   Journal of Chemical Information and Modeling

Unveiling Inherent Degeneracies in Determining Population-Weighted Ensembles of Interdomain Orientational Distributions Using NMR Residual Dipolar Couplings: Application to RNA Helix Junction Helix Motifs

(2015) Shan Yang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings

(2015) Loïc Salmon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective small-molecule inhibition of an RNA structural element

(2015) John A. Howe et al.   NATURE

Development and application of aromatic [13C, 1H] SOFAST-HMQC NMR experiment for nucleic acids

(2014) Bharathwaj Sathyamoorthy et al.   JOURNAL OF BIOMOLECULAR NMR

Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility

(2014) Sheng Tian et al.   Journal of Chemical Information and Modeling

Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery

(2014) Marcus Fischer et al.   Nature Chemistry

Measuring similarity between dynamic ensembles of biomolecules

(2014) Shan Yang et al.   NATURE METHODS

Advances in the Determination of Nucleic Acid Conformational Ensembles

(2013) Loïc Salmon et al.   Annual Review of Physical Chemistry

Exploring the role of receptor flexibility in structure-based drug discovery

(2013) Ferran Feixas et al.   BIOPHYSICAL CHEMISTRY

A General Method for Constructing Atomic-Resolution RNA Ensembles using NMR Residual Dipolar Couplings: The Basis for Interhelical Motions Revealed

(2013) Loïc Salmon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Methods to enable the design of bioactive small molecules targeting RNA

(2013) Matthew D. Disney et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Novel Insights of Structure-Based Modeling for RNA-Targeted Drug Discovery

(2012) Lu Chen et al.   Journal of Chemical Information and Modeling

Potential and Limitations of Ensemble Docking

(2012) Oliver Korb et al.   Journal of Chemical Information and Modeling

Evaluation of DOCK 6 as a pose generation and database enrichment tool

(2012) Scott R. Brozell et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Docking and scoring with ICM: the benchmarking results and strategies for improvement

(2012) Marco A. C. Neves et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

(2012) Michael M. Mysinger et al.   JOURNAL OF MEDICINAL CHEMISTRY

Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening

(2011) Sara E. Nichols et al.   Journal of Chemical Information and Modeling

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

(2011) Andrew C Stelzer et al.   Nature Chemical Biology

3D maps of RNA interhelical junctions

(2011) Maximillian H Bailor et al.   Nature Protocols

Emerging Methods for Ensemble-Based Virtual Screening

(2010) Rommie Amaro et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Accuracy Assessment of Protein-Based Docking Programs against RNA Targets

(2010) Yaozong Li et al.   Journal of Chemical Information and Modeling

Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments

(2010) Ian R. Craig et al.   Journal of Chemical Information and Modeling

Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

(2010) M. H. Bailor et al.   SCIENCE

Strategies for the design of RNA-binding small molecules

(2009) Fareed Aboul-ela   Future Medicinal Chemistry

Recipes for the Selection of Experimental Protein Conformations for Virtual Screening

(2009) Manuel Rueda et al.   Journal of Chemical Information and Modeling

Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition

(2009) Aaron T. Frank et al.   NUCLEIC ACIDS RESEARCH

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

(2009) P. T. Lang et al.   RNA

NMR: prediction of molecular alignment from structure using the PALES software

(2008) Markus Zweckstetter   Nature Protocols

MADAMM: A multistaged docking with an automated molecular modeling protocol

(2008) N. M. F. S. A. Cerqueira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

(2008) O. F. Lange et al.   SCIENCE