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

Sensitivity, Specificity, and Predicted Value01:13

Sensitivity, Specificity, and Predicted Value

In healthcare diagnostics, laboratory tests play a crucial role in identifying and diagnosing a wide range of medical conditions. However, interpreting test results is not always straightforward. An abnormal test result does not always confirm the presence of a disease, just as a normal result does not guarantee its absence. To assess the reliability of these diagnostic tools, healthcare practitioners rely on two key statistical indicators: sensitivity and specificity.
Sensitivity is the...
Dose-Response Relationship: Selectivity and Specificity01:25

Dose-Response Relationship: Selectivity and Specificity

Drugs exert their therapeutic effects by interacting with receptors, enzymes, or ion channels that are present throughout the human body. The strength and duration of the interaction between a drug and its target receptor are characterized by the selectivity and specificity of the drug. Selectivity refers to a drug's strong preference for its intended target over other targets. For instance, isoprenaline, a non-selective β-adrenergic agonist, interacts with both β1- and β2-adrenergic receptors...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Data Validation01:15

Data Validation

Method validation is a crucial process in analytical chemistry designed to confirm that a given method consistently produces reliable and high-quality results. This process is essential when a method is applied to different sample matrices or when procedural modifications are made, ensuring that the results meet acceptable standards across various applications.
Key parameters for method validation include:

You might also read

Related Articles

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

Sort by
Same author

MD2NMR: Linking molecular dynamics with NMR relaxation.

Biophysical journal·2026
Same author

S1P-S1PR1 signaling impairs CD8<sup>+</sup> T cell metabolism and effector function in tumors.

EMBO reports·2026
Same author

Integrating evidence from protein domains to identify cancer driver mutations.

Protein science : a publication of the Protein Society·2026
Same author

G34R cancer mutation alters the conformational ensemble and dynamics of the histone H3.3 tails.

Nucleic acids research·2026
Same author

The endoplasmic reticulum protein FAM134B acts as a regulator of mitochondrial morphology.

Journal of cell science·2025
Same author

Co-Var, a Measure to Determine Intra-protein, Inter-protein, Protein-DNA, or Protein-RNA Coevolution.

Methods in molecular biology (Clifton, N.J.)·2025
Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026
Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026
Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026
Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026
Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026
Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026
See all related articles

Related Experiment Video

Updated: Jun 22, 2026

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

Ensemble approach to predict specificity determinants: benchmarking and validation.

Saikat Chakrabarti1, Anna R Panchenko

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA. chakraba@ncbi.nlm.nih.gov

BMC Bioinformatics
|July 4, 2009
PubMed
Summary
This summary is machine-generated.

Identifying specificity determining sites in proteins is crucial. This study benchmarks prediction methods, finding that reliable predictors identify sites closer to ligands, suggesting functional relevance for mutagenesis.

More Related Videos

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Related Experiment Videos

Last Updated: Jun 22, 2026

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
08:04

Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons

Published on: June 6, 2025

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances
07:35

Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances

Published on: October 11, 2018

Area of Science:

  • Protein bioinformatics
  • Computational biology
  • Molecular evolution

Background:

  • Accurate identification of specificity determining sites (SDSs) in protein families is critical for understanding functional specification and diversification.
  • Existing methods for predicting SDSs require rigorous evaluation to ensure reliability.
  • This study addresses the challenge of identifying functionally important sites within protein families.

Purpose of the Study:

  • To rigorously evaluate and benchmark methods for predicting specificity determining sites.
  • To identify novel potential specificity determining sites using an ensemble approach.
  • To assess the functional relevance of predicted sites through structural analysis.

Main Methods:

  • Comparative benchmarking of multiple prediction methods using a standardized protocol.
  • Application of the top-performing methods in an ensemble strategy.
  • Analysis of structural characteristics of predicted specificity determining sites in relation to ligands.

Main Results:

  • A comparative benchmarking protocol was established to reliably evaluate prediction methods.
  • Structural analysis revealed that more reliable prediction methods identify SDSs that are closer to each other and to the ligand.
  • Similarities in structural features between predicted and actual protein subsites were observed.

Conclusions:

  • The structural characteristics of predicted SDSs can serve as a validation metric for prediction accuracy.
  • The identified potential SDSs may be indirectly involved in specific molecular interactions.
  • These potential SDSs represent promising targets for future mutagenesis experiments to confirm functional roles.