Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Jun 24, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

DOCK 6: combining techniques to model RNA-small molecule complexes.

P Therese Lang¹, Scott R Brozell, Sudipto Mukherjee

¹Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, California 94143, USA.

RNA (New York, N.Y.)

|April 17, 2009

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

A new NMR protocol for estimating protein side chain rotameric preferences using <sup>1</sup>H relaxation and J couplings.

Journal of magnetic resonance (San Diego, Calif. : 1997)·2026

Same author

Cytokine receptor and JAK/STAT pathway mutations in acute myeloid leukemia: Prevalence and clinical impact.

Cancer·2026

Same author

Why detailed modeling matters in the FE-based pre-clinical evaluation of temporomandibular joint implants.

Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery·2026

Same author

Morphometric variations of human mandible in the Indian population: comparison between healthy and ankylosed temporomandibular joints.

Journal of cranio-maxillo-facial surgery : official publication of the European Association for Cranio-Maxillo-Facial Surgery·2026

Same author

Biallelic germline MBD4 mutations predispose to colorectal polyposis, hypermutated AML, and schwannomas.

Familial cancer·2026

Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026

Same journal

Optimized tRNA structure-seq reveals robust tRNA secondary structures in <i>S. cerevisiae</i> under mild stress conditions.

RNA (New York, N.Y.)·2026

Same journal

SERIPH: A Two-Step Extraction Protocol for Selective Enrichment of Semi-Extractable RNAs.

RNA (New York, N.Y.)·2026

Same journal

Reduced Sensitivity to RNA Structural Differences Distinguishes Eukaryotic Pus4 from Bacterial TruB.

RNA (New York, N.Y.)·2026

Same journal

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.

RNA (New York, N.Y.)·2026

Same journal

RBM38 Regulates HORMAD1 Splicing to Enhances MEK Inhibitor Sensitivity in Breast Cancer.

RNA (New York, N.Y.)·2026

Same journal

EF-P Inhibits Ribosomal α-Hydroxy Acid Incorporation: Strategic tRNA Body Selection for Co-incorporating α-Hydroxy Acids and Nonproteinogenic Amino Acids into Depsipeptides.

RNA (New York, N.Y.)·2026

See all related articles

The DOCK suite can be adapted for RNA-ligand docking, achieving high accuracy in recreating binding poses. Optimized parameters and scoring functions improve success rates for structure-based RNA drug design.

Area of Science:

Computational Chemistry
Structural Biology
Drug Discovery

Background:

Growing interest in RNA therapeutics necessitates tools for RNA-targeted drug design.
Existing protein-ligand docking algorithms require adaptation for nucleic acids.

Purpose of the Study:

To validate the DOCK suite's ability to accurately predict RNA-ligand binding poses.
To assess the performance of DOCK with optimized parameters and scoring functions for RNA targets.

Main Methods:

Compiled a test set of experimentally determined RNA-ligand complexes.
Utilized the DOCK suite with optimized parameters and a minimal scoring function.
Rescored docked conformations using implicit solvent models (AMBER GB/SA, PB/SA) with explicit water and ions.

More Related Videos

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Practical Aspects of Sample Preparation and Setup of ¹H R_1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Related Experiment Videos

Last Updated: Jun 24, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Practical Aspects of Sample Preparation and Setup of ¹H R_1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Main Results:

DOCK successfully recreated binding poses within 2 Å heavy-atom RMSD for 70% (≤7 rotatable bonds) and 26% (≤13 rotatable bonds) of the test set.
Rescoring with implicit solvent models improved success rates to 80% (PB/SA, ≤7 bonds), 58% (GB/SA, ≤13 bonds), and 47% (PB/SA, ≤13 bonds).

Conclusions:

The DOCK suite is a viable tool for structure-based drug design targeting RNA.
RNA-ligand interactions present unique electrostatic properties that can be managed through appropriate potential functions.
New DOCK functions can be readily incorporated to address emerging scientific challenges.