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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...

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....

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...

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Updated: Jul 9, 2025

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

DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model.

Yitian Fang^1,2, Yi Jiang³, Leyi Wei⁴

¹State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200040, China.

Bioinformatics (Oxford, England)

|November 28, 2023

Summary

DeepProSite accurately identifies protein binding sites using both structure and sequence data. This new framework improves upon existing methods and demonstrates broad applicability for drug design and biological research.

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Area of Science:

Computational biology
Structural bioinformatics
Drug discovery

Background:

Identifying protein binding sites is essential for understanding biological processes and developing new drugs.
Current sequence-based methods lack accuracy due to limited feature consideration and absence of structural information.

Purpose of the Study:

To introduce DeepProSite, a novel framework for enhanced protein binding site identification.
To leverage both protein structure and sequence data for improved prediction accuracy.

Main Methods:

DeepProSite integrates protein structures from ESMFold and sequence representations from language models.
Utilizes a Graph Transformer architecture for binding site prediction as graph node classifications.
Evaluates performance against state-of-the-art sequence- and structure-based methods.

Main Results:

DeepProSite outperforms existing methods in predicting protein-protein and protein-peptide binding sites.
Demonstrates robust performance on unbound structures, unlike competing methods.
Shows generalization capability by successfully predicting binding sites for nucleic acids and other ligands.

Conclusions:

DeepProSite offers a significant advancement in protein binding site prediction accuracy and reliability.
The framework's versatility extends to various ligand types, highlighting its broad utility.
An online server is available for practical application of DeepProSite.