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 Experiment Videos

SitesBase: a database for structure-based protein-ligand binding site comparisons.

Nicola D Gold1, Richard M Jackson

  • 1Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.

Nucleic Acids Research
|December 31, 2005
PubMed
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

BAYESIAN ALIGNMENT OF SIMILARITY SHAPES.

The annals of applied statistics·2013
Same author

Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities.

The journal of physical chemistry. B·2012
Same author

Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable.

PloS one·2012
Same author

Correction to "Machine learning-based method to improve docking scoring functions and its application to drug repurposing".

Journal of chemical information and modeling·2011
Same author

ReverseScreen3D: a structure-based ligand matching method to identify protein targets.

Journal of chemical information and modeling·2011
Same author

A machine learning-based method to improve docking scoring functions and its application to drug repurposing.

Journal of chemical information and modeling·2011
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

SitesBase is a new database that helps predict how proteins recognize small molecules by comparing protein-ligand binding sites. This tool aids in understanding protein function and molecular recognition.

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein function is governed by various cellular components.
  • Molecular recognition of small molecules is crucial for protein activity.
  • Predicting protein-ligand interactions is a key challenge in structural biology.

Purpose of the Study:

  • To introduce SitesBase, a novel database for analyzing structural similarities between protein-ligand binding sites.
  • To facilitate the prediction of common molecular recognition patterns.
  • To enable deeper insights into protein structure-function relationships.

Main Methods:

  • Development of a user-friendly database, SitesBase.
  • Inclusion of structural similarity data for known ligand binding sites from the Protein Data Bank.

Related Experiment Videos

  • Accessibility of the database for community-wide analysis.

    • Main Results:

    • SitesBase provides easily accessible information on structural similarities between protein-ligand binding sites.
    • The database enables the identification of common recognition motifs.
    • Facilitates comparative analysis of binding site structures.

    Conclusions:

    • SitesBase is a valuable resource for researchers studying molecular recognition.
    • The database supports the exploration of protein structure-function relationships.
    • Promotes wider understanding of how proteins interact with small molecules.