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Conserved Binding Sites01:49

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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.
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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.
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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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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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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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Updated: Jul 5, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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Seq-InSite: sequence supersedes structure for protein interaction site prediction.

SeyedMohsen Hosseini1, G Brian Golding2, Lucian Ilie1

  • 1Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada.

Bioinformatics (Oxford, England)
|January 12, 2024
PubMed
Summary

Predicting protein interaction sites is crucial for understanding cellular functions. A new sequence-based tool, Seq-InSite, achieves high accuracy without needing protein structures, offering a widely applicable solution.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Protein structure and function

Background:

  • Protein interactions are fundamental to cellular processes.
  • Experimental methods for identifying interaction sites are costly and time-consuming.
  • Computational prediction methods exist, but often trade accuracy for applicability.

Purpose of the Study:

  • To develop a computational tool for predicting protein interaction sites.
  • To achieve high accuracy comparable to structure-based methods using only sequence data.
  • To create a widely applicable tool for protein interaction site prediction.

Main Methods:

  • Development of a novel sequence-based computational program, Seq-InSite.
  • Utilizing evolutionary conservation analysis for prediction validation.
  • Comparison against existing state-of-the-art structure-based predictors.

Main Results:

  • Seq-InSite demonstrates superior performance compared to existing sequence-based models.
  • The accuracy of Seq-InSite matches that of state-of-the-art structure-based predictors.
  • Seq-InSite effectively eliminates the need for protein structural data in prediction.

Conclusions:

  • Seq-InSite represents a significant advancement in sequence-based protein interaction site prediction.
  • The tool offers a powerful and broadly applicable solution for researchers.
  • Seq-InSite is freely available as a web server and open-source code.