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

Related Concept Videos

Affinity and Avidity

Affinity and Avidity

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

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:

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

Electron Affinity

Electron Affinity

The electron affinity (EA) is the energy change for adding an electron to a gaseous atom to form an anion (negative ion).

Conserved Binding Sites

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...

Affinity Chromatography

Affinity Chromatography

Affinity chromatography is a powerful technique extensively utilized for separating and purifying specific biomolecules from complex mixtures. It capitalizes on the highly selective binding between an analyte and its counterpart, such as antibody-antigen interactions. The counterpart is immobilized on the stationary phase, forming an affinity column. The stationary phase typically consists of solid support, such as agarose or porous glass beads, immobilizing the affinity ligand. The mobile...

You might also read

Related Articles

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

Sort by

Same author

The role of health institutions in the epidemiological surveillance of arboviral diseases in Rio Grande do Sul, Brazil: notification, hospitalization, and regional differences.

BMC public health·2026

Same author

Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.

Pharmaceuticals (Basel, Switzerland)·2025

Same author

A Primer on SAnDReS 2.0 for Scoring Function Design.

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

Same author

Exploring the Scoring Function Space with Lasso Regression.

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

Same author

Combining MVD and Ridge Method to Predict CDK2 Inhibition.

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

Same author

Elastic Net Regression to Predict CDK2 Inhibition.

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

Same journal

How Do DICER1 Syndrome Mutations Disrupt Catalysis? Unveiling Dicer Metal Binding Architecture and Mechanism of Action Using MD Simulations and QM/MM Calculations.

Journal of computational chemistry·2026

Same journal

Quadruple Bonding of Alkaline Earth Atoms in AeCLi<sub>4</sub> (Ae = Be - Ba) Complexes.

Journal of computational chemistry·2026

Same journal

From SMILES Codes for Reactants and Products to Transition States With VeloxChem.

Journal of computational chemistry·2026

Same journal

Electric-Field Effects on Structure and Conductance in a Cytochrome b<sub>562</sub> Junction.

Journal of computational chemistry·2026

Same journal

Quantum Chemistry Study of Luminescence Quenching in the Eu<sup>3+</sup>@UiO-67 Sensor Induced by Ag<sup>+</sup> Ions.

Journal of computational chemistry·2026

Same journal

Projection-Modified Direct Inversion in the Iterative Subspace: A Memory-Efficient Convergence Method for the Extended Molecular Ornstein-Zernike Theory.

Journal of computational chemistry·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 20, 2026

Determining Binding Affinity KD of Radiolabeled Antibodies to Immobilized Antigens

Determining Binding Affinity KD of Radiolabeled Antibodies to Immobilized Antigens

Published on: June 23, 2022

Taba: A Tool to Analyze the Binding Affinity.

Amauri Duarte da Silva^1,2, Gabriela Bitencourt-Ferreira¹, Walter Filgueira de Azevedo^1,2

¹Laboratory of Computational Systems Biology, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Ipiranga Avenue, 6681 Partenon, 90619-900, Porto Alegre/RS, Brazil.

Journal of Computational Chemistry

|August 15, 2019

Summary

This summary is machine-generated.

This study introduces Taba, a novel computational method combining mass-spring systems and machine learning to predict protein-ligand binding affinity. Taba offers superior accuracy compared to existing tools for targeted protein systems.

Keywords:

binding affinity drug design machine learning protein-ligand interactions scoring function

More Related Videos

Comparing the Affinity of GTPase-binding Proteins using Competition Assays

Comparing the Affinity of GTPase-binding Proteins using Competition Assays

Published on: October 8, 2015

Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis

Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis

Published on: August 15, 2013

Related Experiment Videos

Last Updated: Jan 20, 2026

Determining Binding Affinity KD of Radiolabeled Antibodies to Immobilized Antigens

Determining Binding Affinity KD of Radiolabeled Antibodies to Immobilized Antigens

Published on: June 23, 2022

Comparing the Affinity of GTPase-binding Proteins using Competition Assays

Comparing the Affinity of GTPase-binding Proteins using Competition Assays

Published on: October 8, 2015

Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis

Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis

Published on: August 15, 2013

Area of Science:

Computational chemistry
Structural biology
Machine learning

Background:

Predicting protein-ligand binding affinity computationally is challenging.
Crystallographic structures and binding data enable system-specific machine learning models.

Purpose of the Study:

To develop a new methodology for predicting protein-ligand binding affinity.
To create a machine learning model targeted to specific protein systems.

Main Methods:

A novel approach combining a mass-spring system with supervised machine learning.
Exploration of the scoring function space for targeted model generation.
Implementation in a new Python program named Taba.

Main Results:

The new model demonstrates superior predictive performance.
Outperforms classical scoring functions in Molegro Virtual Docker, AutoDock4, and AutoDock Vina.
A new program, Taba, was developed and made publicly available.

Conclusions:

The Taba methodology provides an effective way to predict binding affinity for specific protein systems.
Offers a valuable tool for computational drug discovery and structural biology research.