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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 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...

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...

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...

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 polypeptide...

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Related Experiment Video

Updated: Jun 11, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Predicting unknown binding sites for transition-metal-based compounds in proteins.

Andrea Levy¹, Ursula Rothlisberger¹

¹Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

|June 9, 2026

Summary

This summary is machine-generated.

Predicting transition metal binding sites in proteins is challenging. Two computational tools, Metal3D and Metal1D, show promise for identifying potential binding hotspots, aiding drug discovery for cancer therapeutics.

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Published on: September 7, 2019

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Last Updated: Jun 11, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

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Published on: January 26, 2024

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Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Ion Mobility-Mass Spectrometry Techniques for Determining the Structure and Mechanisms of Metal Ion Recognition and Redox Activity of Metal Binding Oligopeptides

Published on: September 7, 2019

Area of Science:

Biochemistry
Computational Chemistry
Drug Discovery

Background:

Transition-metal compounds show therapeutic potential, especially in oncology.
Accurate prediction of metal ion binding sites in proteins is crucial but difficult.

Purpose of the Study:

To evaluate Metal3D and Metal1D tools for predicting transition metal binding sites in proteins.
To assess the utility of these predictors for identifying potential therapeutic binding hotspots.

Main Methods:

Testing Metal3D and Metal1D on apo protein structures with known transition metal binding sites.
Analyzing the accuracy of the predictors in identifying experimentally validated binding locations.

Main Results:

Both Metal3D and Metal1D successfully identified at least one experimentally observed binding site for transition metal complexes.
The predictors' performance was sensitive to side-chain conformations, indicating limitations.

Conclusions:

Metal3D and Metal1D offer a rapid, low-cost method for initial identification of transition metal binding hotspots.
Further refinement using more computationally intensive methods is suggested for improved accuracy.