Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA as a Genetic Template02:05

DNA as a Genetic Template

27.4K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
27.4K
DNA as a Genetic Template02:05

DNA as a Genetic Template

9.4K
9.4K
Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

32.6K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
32.6K
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

10.8K
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
10.8K
From DNA to Protein03:06

From DNA to Protein

22.2K
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
22.2K
RNA Editing02:23

RNA Editing

9.8K
RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
9.8K

You might also read

Related Articles

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

Sort by
Same author

scDifformer: diffusion-based post-training for virtual cell modeling across large-scale single-cell data.

Nucleic acids research·2026
Same author

Anti-PD-1 monoclonal antibody suppresses hepatitis B virus in patients with hepatocellular carcinoma.

Chinese medical journal·2026
Same author

Causal Prediction of TP53 Variant Pathogenicity Using a Perturbation-Informed Protein Language Model.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026
Same author

Association between lactate-to-albumin ratio and all-cause mortality in patients with cerebrovascular disease: A retrospective cohort study.

Medicine·2025
Same author

The multidimensional role of laminin γ2 (LAMC2) on cancer progression.

Cancer genetics·2025
Same author

Advancing biological understanding of cellular senescence with computational multiomics.

Nature genetics·2025

Related Experiment Video

Updated: Jan 23, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.2K

P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking.

Jinfang Zheng1, Xu Hong1, Juan Xie1

  • 1School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.

Bioinformatics (Oxford, England)
|June 8, 2019
PubMed
Summary

We developed P3DOCK, a novel protein-RNA docking method integrating free and template-based docking strategies. P3DOCK significantly improves prediction accuracy and success rates for modeling complex three-dimensional structures.

More Related Videos

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology
10:25

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology

Published on: November 22, 2024

636
A Salt-Templated Synthesis Method for Porous Platinum-based Macrobeams and Macrotubes
13:08

A Salt-Templated Synthesis Method for Porous Platinum-based Macrobeams and Macrotubes

Published on: May 18, 2020

9.6K

Related Experiment Videos

Last Updated: Jan 23, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

1.2K
Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology
10:25

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology

Published on: November 22, 2024

636
A Salt-Templated Synthesis Method for Porous Platinum-based Macrobeams and Macrotubes
13:08

A Salt-Templated Synthesis Method for Porous Platinum-based Macrobeams and Macrotubes

Published on: May 18, 2020

9.6K

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Protein-RNA interactions are crucial for gene regulation.
  • Understanding these interactions requires accurate three-dimensional (3D) structural modeling.
  • Atomic-level details in protein-RNA complexes are vital for functional insights.

Purpose of the Study:

  • To compare free and template-based docking algorithms for protein-RNA complexes.
  • To develop an integrated docking approach combining the strengths of both methods.
  • To enhance the accuracy and success rate of protein-RNA structure prediction.

Main Methods:

  • Comparative analysis of free docking and template-based docking algorithms.
  • Integration of complementary docking strategies into a novel algorithm, P3DOCK.
  • Validation using three independent protein-RNA docking benchmarks.
  • Application of hierarchical clustering to refine docking predictions.

Main Results:

  • P3DOCK outperforms individual free and template-based docking methods.
  • The integrated approach demonstrates a higher success rate (3-20%) compared to state-of-the-art methods.
  • Hierarchical clustering further improves the success rate of P3DOCK predictions.
  • A user-friendly webserver and benchmark dataset are provided.

Conclusions:

  • Integrating free and template-based docking significantly enhances protein-RNA structure prediction.
  • P3DOCK offers a more accurate and reliable method for modeling protein-RNA complexes.
  • The developed tools facilitate further research in gene regulation and molecular interactions.