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Protein-protein Interfaces

Protein-protein Interfaces

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...

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...

Protein Networks

Protein Networks

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,...

Ligand Binding Sites

Ligand Binding Sites

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...

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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:

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Related Experiment Video

Updated: May 8, 2025

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

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

Published on: January 26, 2024

PCANN Program for Structure-Based Prediction of Protein-Protein Binding Affinity: Comparison

Olga O Lebedenko¹, Mikhail S Polovinkin¹, Anastasiia A Kazovskaia^1,2

¹Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia.

|March 21, 2025

Summary

This summary is machine-generated.

We developed PCANN, a new AI tool for predicting protein-protein binding affinity using neural networks. PCANN outperforms existing methods, offering a more accurate approach for understanding protein interactions.

Keywords:

ESM‐2 language model Kd prediction program comparison of Kd predictors deep learning graph attention network protein binding databases protein–protein binding

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Last Updated: May 8, 2025

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

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

Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Area of Science:

Computational biology
Structural bioinformatics
Artificial intelligence in drug discovery

Background:

Accurate prediction of protein-protein binding affinity is crucial for understanding biological processes and developing therapeutics.
Existing computational predictors face limitations due to data scarcity and accuracy issues.

Purpose of the Study:

To introduce PCANN, a novel structure-based predictor for protein-protein complex affinity.
To evaluate PCANN's performance against existing state-of-the-art methods.

Main Methods:

Utilized the ESM-2 language model to encode protein binding interface information.
Employed a graph attention network (GAT) for affinity prediction.
Trained and tested PCANN on two novel literature-extracted datasets.

Main Results:

PCANN demonstrated superior performance compared to the publicly available predictor BindPPI.
Achieved a mean absolute error (MAE) of 1.3 kcal/mol, outperforming BindPPI's 1.4 kcal/mol.

Conclusions:

PCANN represents a significant advancement in structure-based affinity prediction for protein complexes.
Addressing data limitations through AI-leveraged literature search and human curation can further improve deep learning-based predictors.