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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Ligand Binding Sites02:40

Ligand Binding Sites

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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.
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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Protein Networks02:26

Protein Networks

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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.
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Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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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...
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Updated: May 12, 2025

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

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InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep.

Fabien Mareuil1, Rachel Torchet1, Luis Checa Ruano2

  • 1Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015 Paris, France.

Nucleic Acids Research
|May 8, 2025
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Summary
This summary is machine-generated.

InDeepNet predicts protein binding sites and their suitability for drug development. This platform aids researchers in identifying potential drug targets by assessing protein-ligand interactions and conformational changes.

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Area of Science:

  • Computational biology
  • Structural biology
  • Drug discovery

Background:

  • Predicting protein binding sites is essential for understanding protein-protein interactions (PPIs) and identifying drug targets.
  • Existing computational methods often struggle to evaluate the ligandability of PPIs, particularly considering conformational changes.

Purpose of the Study:

  • To introduce InDeepNet, a web-based platform that integrates deep learning for binding site prediction with an assessment of ligand-bound conformations.
  • To provide researchers with an accessible tool for predicting binding sites and evaluating their potential for small-molecule binding, thereby enhancing structure-based drug design.

Main Methods:

  • Developed InDeepNet, a platform combining the InDeep deep-learning model for binding site prediction and InDeepHolo for evaluating ligand-bound (holo) conformations.
  • Enabled users to upload protein structures from various sources (in-house, PDB, AlphaFold) for analysis.
  • Integrated Mol* for interactive 3D visualization of predicted binding sites.

Main Results:

  • InDeepNet successfully predicts potential binding sites for proteins and small molecules.
  • The platform facilitates the selection of optimal conformations for small-molecule binding, crucial for drug design.
  • InDeepNet offers an intuitive interface, eliminating the need for specialized coding or high-performance computing.

Conclusions:

  • InDeepNet streamlines the assessment of PPI targets and ligandability prediction.
  • The platform democratizes access to advanced predictive modeling for drug discovery and therapeutic development targeting PPIs.