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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...

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-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...

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Allosteric Proteins-ATCase

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...

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: Aug 16, 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

DeepBSRPred: deep learning-based binding site residue prediction for proteins.

Rahul Nikam¹, Kumar Yugandhar^1,2, M Michael Gromiha^3,4

¹Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, 600036, India.

|December 27, 2022

Summary

This summary is machine-generated.

DeepBSRPred, a deep neural network method, accurately predicts protein-protein interaction binding sites using sequence and structure data. This advancement aids in understanding protein complex functions and binding affinities.

Keywords:

AlphaFold Binding sites Deep learning Neural network Protein–protein interactions

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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

Area of Science:

Computational Biology
Bioinformatics
Structural Biology

Background:

Protein-protein interactions (PPIs) are crucial for cellular functions.
Identifying binding sites on proteins is key to understanding complex formation, affinities, and functions.

Purpose of the Study:

To develop a novel deep neural network-based method, DeepBSRPred, for predicting protein binding sites.
To leverage both protein sequence and predicted structural information for enhanced prediction accuracy.

Main Methods:

Utilized a deep neural network architecture.
Incorporated sequence-based features like Position-Specific Scoring Matrix (PSSM) and conservation scores.
Integrated structure-based features such as solvent accessible surface area and residue depth, derived from AlphaFold2 predictions.

Main Results:

Achieved an average F1 score of 0.73 on a dataset of 1236 proteins.
Demonstrated superior performance compared to existing methods across four benchmark datasets.
DeepBSRPred effectively predicts binding sites using integrated sequence and structure features.

Conclusions:

DeepBSRPred offers a powerful and accurate approach for predicting protein binding sites.
The method enhances the understanding of protein-protein interactions and their functional implications.
The developed web server and source code are publicly available for research use.