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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 analyses the...

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 analyses the...

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 the...

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.
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...

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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.
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

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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 polypeptide...

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Related Experiment Video

Updated: Jun 9, 2026

Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms

Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms

Published on: April 17, 2017

Large-scale comparison of four binding site detection algorithms.

Peter Schmidtke¹, Catherine Souaille, Frédéric Estienne

¹Sanofi-Aventis VA Research Centre, Structure Design & Informatics, 13 quai Jules Guesde, BP14, 94403 Vitry-sur-Seine, France.

Journal of Chemical Information and Modeling

|September 11, 2010

Summary

Four cavity detection algorithms were compared. fpocket showed the highest accuracy in predicting protein binding sites, while PocketFinder and SiteFinder performed best on apo structures.

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Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Accurate identification of protein binding sites is crucial for drug discovery and understanding protein function.
Several algorithms exist for predicting these cavities, but their comparative performance needs rigorous evaluation.

Purpose of the Study:

To conduct a large-scale evaluation and comparison of four prominent cavity detection algorithms: SiteFinder, fpocket, PocketFinder, and SiteMap.
To assess algorithm performance on both protein-ligand complexes (holo) and unbound protein structures (apo).

Main Methods:

Evaluation of SiteFinder, fpocket, PocketFinder, and SiteMap on a dataset of 5416 holo and 9900 apo protein structures.
Analysis of pocket identification rates and binding site ranking accuracy.
Measurement of computational time for each algorithm.

Main Results:

All four algorithms identified approximately 95% of pockets in holo structures.
SiteFinder (optimized), SiteMap, and fpocket demonstrated comparable pocket ranking performance.
PocketFinder and SiteFinder (optimized) excelled in identifying binding sites in apo structures, with 96% and 84% accuracy, respectively.
fpocket demonstrated the highest prediction accuracy overall.
SiteFinder exhibited the fastest calculation time (1.6 s), significantly outperforming SiteMap (2 min).

Conclusions:

fpocket is the most accurate algorithm for binding site prediction among those evaluated.
SiteFinder offers a compelling balance of speed and accuracy, particularly for apo structures.
Algorithm choice may depend on whether holo or apo structures are being analyzed and the priority of speed versus accuracy.