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

Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
Ligand Binding Sites02:40

Ligand Binding Sites

12.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.9K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
Protein Networks02:26

Protein Networks

4.0K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.0K
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

196
Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
196
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

12.9K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.9K

You might also read

Related Articles

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

Sort by
Same author

Engineered immune cells and extracellular vesicles target tumour microenvironment barriers in solid tumour immunotherapy.

Discover oncology·2026
Same author

Physical activity and academic burnout among middle school students: uncovering cognitive reappraisal and expressive suppression.

Frontiers in psychology·2026
Same author

Ultrasensitive Detection of Porcine Epidemic Diarrhea Virus Infections Using Multivalent DNA Nanostructure-Enabled Lateral Flow Assay.

Advanced healthcare materials·2026
Same author

Self-adjuvanting α-helical polypeptide simultaneously delivers neoantigen mRNAs and activates dendritic cells to eradicate tumors.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Selective capture and digital counting of intact HIV pseudovirus using designer DNA nets, tethered motion, and photonic resonator interferometric scattering microscopy.

APL bioengineering·2026
Same author

Identification of a Novel MTM1 Mutation Associated with X-Linked Myotubular Myopathy: Clinical and Molecular Insights for Prenatal Diagnosis.

International journal of women's health·2026
Same journal

Advancing Biochemical Molecule Registration, Representation and Search for New Drug Modalities.

Journal of chemical information and modeling·2026
Same journal

A Unified Molecular Graph and Protein Language Model Framework for Predicting Human Drug-Hormone Receptor Interactions with Structure-Aware Validation.

Journal of chemical information and modeling·2026
Same journal

Intricate Role of Cholesterol in Membrane Fusion.

Journal of chemical information and modeling·2026
Same journal

tmGNN-XAI: An Explainable Graph Neural Network Tool for Predicting Electronic Properties of Transition Metal Complexes from SMILES.

Journal of chemical information and modeling·2026
Same journal

QSAR in the Browser: An Interactive Cheminformatics Web Application.

Journal of chemical information and modeling·2026
Same journal

FoldDoF: Utilizing the Primary Degrees of Freedom of Protein Backbone for Geometric Modeling and Generation.

Journal of chemical information and modeling·2026
See all related articles

Related Experiment Video

Updated: Jul 7, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

1.9K

APIPred: An XGBoost-Based Method for Predicting Aptamer-Protein Interactions.

Zheng Fang1,2,3, Zhongqi Wu1,2,4, Xinbo Wu5

  • 1Holonyak Micro and Nanotechnology Lab (HMNTL), University of Illinois at Urbana-Champaign, Champaign-Urbana 61801, United States.

Journal of Chemical Information and Modeling
|December 21, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a computational method to predict aptamer-protein interactions, accelerating the discovery of aptamers for biosensing and disease therapies. The new model achieves high accuracy, improving upon existing techniques.

More Related Videos

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses
12:23

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

Published on: September 7, 2022

1.7K
Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

10.6K

Related Experiment Videos

Last Updated: Jul 7, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

1.9K
In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses
12:23

In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

Published on: September 7, 2022

1.7K
Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis
08:09

Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

Published on: January 7, 2017

10.6K

Area of Science:

  • Biotechnology
  • Computational Biology
  • Bioinformatics

Background:

  • Aptamers, single-stranded DNA or RNA oligonucleotides, offer high specificity for target binding and are crucial in biosensing and disease therapies.
  • The traditional aptamer generation process, SELEX (Systematic Evolution of Ligands by Exponential Enrichment), is lengthy and resource-intensive.

Purpose of the Study:

  • To develop and validate computational models for predicting aptamer-protein interactions, thereby accelerating aptamer selection.
  • To improve the efficiency and reduce the time required for identifying functional aptamers for therapeutic and diagnostic applications.

Main Methods:

  • Utilized in silico and computational tools to analyze protein and aptamer pair data.
  • Developed and evaluated multiple machine-learning models for predicting aptamer-protein interactions.
  • Validated model predictions using molecular docking and Surface Plasmon Resonance (SPR) binding assays.

Main Results:

  • Achieved high prediction accuracy (96.5%) and precision (97%) with one developed machine-learning model, surpassing previous benchmarks.
  • Demonstrated the robustness of the APIPred algorithm through experimental validation via molecular docking and SPR assays.
  • The model effectively predicts aptamer-protein binding selectivity.

Conclusions:

  • The developed computational approach significantly enhances the prediction of aptamer-protein interactions.
  • This high-throughput screening model offers a rapid method for identifying aptamer candidates for targeting diseases like cancer and viral epidemics.
  • The APIPred algorithm provides a valuable tool for advancing aptamer-based diagnostics and therapeutics.