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 Networks02:26

Protein Networks

4.6K
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,...
4.6K
Factors Affecting Protein-Drug Binding: Drug Interactions01:23

Factors Affecting Protein-Drug Binding: Drug Interactions

611
Drug interactions are a critical aspect of pharmacology and can occur when two or more drugs compete for the same binding site. This competition can result in one drug displacing another, altering the effect of the displaced drug. Drug interactions are complex processes that rely heavily on how much of the displacer drug is present and how strongly it can bind to the same sites as the displaced drug.
Displacement interactions can have varying outcomes, ranging from toxicity to virtually...
611
Protein and Protein Structure02:15

Protein and Protein Structure

88.6K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
88.6K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.8K
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...
14.8K
Factors Affecting Protein-Drug Binding: Protein-Related Factors01:20

Factors Affecting Protein-Drug Binding: Protein-Related Factors

576
Drug binding to proteins is a key aspect of pharmacokinetics and can influence a drug's distribution, absorption, and elimination in the body. Several factors, including the drug's physiochemical properties, protein concentration, disease states, and the number of binding sites on the protein, influence this process.
The physicochemical properties of a drug play a significant role in its ability to bind to proteins. Lipophilic drugs, which dissolve in fats, oils, and lipids, can be...
576
Affinity and Avidity01:41

Affinity and Avidity

39.2K
Overview
39.2K

You might also read

Related Articles

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

Sort by
Same author

Decoding variants of uncertain significance in systemic autoinflammatory diseases.

Nature reviews. Rheumatology·2026
Same author

Proteome-wide prediction of the functional impact of missense variants with ProteoCast.

Nature communications·2026
Same author

Scaling the profile of life by function with SPIN.

Bioinformatics advances·2026
Same author

ProteoCast: a web server to predict, validate, and interpret missense variant effects.

Journal of molecular biology·2026
Same author

SpeckSeq enables high-throughput functional stratification of MEFV variants in autoinflammatory diseases.

The Journal of experimental medicine·2025
Same author

Editorial overview: Protein-nucleic acid interactions: From origins to design.

Current opinion in structural biology·2025

Related Experiment Video

Updated: Feb 10, 2026

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

2.6K

Local Interaction Signal Analysis Predicts Protein-Protein Binding Affinity.

Raffaele Raucci1, Elodie Laine2, Alessandra Carbone3

  • 1Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 4 Place Jussieu, 75005 Paris, France; Sorbonne Université, Institut des Sciences du Calcul et des Données (ISCD), 75005 Paris, France.

Structure (London, England : 1993)
|May 22, 2018
PubMed
Summary
This summary is machine-generated.

We developed a new model, Local Interaction Signal Analysis (LISA), to accurately predict protein-protein binding energy by analyzing interface geometry. This method improves upon existing models for understanding complex molecular interactions.

Keywords:
atom-atom contactbinding affinitydensity functional theoryelectron densityfavorable contactnon-covalent interactionnon-interacting surfaceprotein interfaceprotein-protein interactionreduced density gradient

More Related Videos

Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification BiCAP
06:45

Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification BiCAP

Published on: June 15, 2018

8.0K
Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis
10:22

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

Published on: August 15, 2013

31.3K

Related Experiment Videos

Last Updated: Feb 10, 2026

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

2.6K
Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification BiCAP
06:45

Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification BiCAP

Published on: June 15, 2018

8.0K
Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis
10:22

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

Published on: August 15, 2013

31.3K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Accurate estimation of protein-protein binding energy is crucial for understanding biological processes.
  • Existing models often struggle to capture the complex energetic contributions at protein interfaces.

Purpose of the Study:

  • To introduce and validate an improved model for predicting protein-protein binding energy.
  • To leverage the geometric and chemical properties of protein-protein interfaces for enhanced prediction accuracy.

Main Methods:

  • Developed Local Interaction Signal Analysis (LISA), a radial function incorporating density functional theory, interface residue distribution, charged residue interactions, and secondary structure contributions.
  • Numerically evaluated the 3D organization of contacts and their contribution to localized hot-sites.
  • Tested LISA on 125 protein complexes with experimental binding energy measurements.

Main Results:

  • LISA achieved a high correlation of 0.81 with experimental binding energies (RMSE of 2.35 ± 0.38 kcal/mol).
  • Model performance remained stable across different functional compositions and conformational changes.
  • A large-scale comparison showed LISA outperformed 17 other existing functions.

Conclusions:

  • LISA provides a powerful geometrical model for understanding protein complex binding energy.
  • The method offers improved accuracy and stability compared to previous approaches.
  • This advancement aids in deciphering the molecular mechanisms of protein interactions.