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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...

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...

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...

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...

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Related Experiment Video

Updated: Jul 3, 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

Using protein binding site prediction to improve protein docking.

Bingding Huang¹, Michael Schroeder

¹Bioinformatics Group, Biotechnological Center, Technical University Dresden, Germany. bhuang@biotec.tu-dresden.de

|July 12, 2008

Summary

This summary is machine-generated.

A new meta server, metaPPI, significantly enhances protein interface prediction accuracy. This improved prediction aids protein docking, boosting candidate generation and ranking for enzyme-inhibitor complexes.

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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

Area of Science:

Computational Biology
Structural Bioinformatics
Protein Science

Background:

Protein-protein interactions are crucial for biological processes.
Accurate prediction of protein interaction interfaces is essential for understanding protein function and complex formation.
Existing tools for interface prediction show limited success rates, particularly for non-enzyme-inhibitor interactions.

Purpose of the Study:

To develop a meta server, metaPPI, for improving protein interaction interface prediction.
To enhance protein docking by integrating predicted interfaces into the candidate generation and ranking stages.
To refine docking scoring for enzyme-inhibitor complexes using geometric features.

Main Methods:

Development of metaPPI, a meta server aggregating multiple interface prediction tools.
Integration of metaPPI predictions to filter candidate poses in rigid-body protein docking based on shape complementarity.
Application of a geometric scoring function rewarding deep pockets for ranking enzyme-inhibitor complex docking solutions.

Main Results:

metaPPI achieves significantly higher prediction success rates: 70% for enzyme-inhibitor and 44% for other interfaces.
Filtering docking candidates with predicted interfaces substantially improves candidate generation.
Geometric scoring further refines the ranking of docking solutions for enzyme-inhibitor complexes.

Conclusions:

metaPPI offers a substantial improvement in protein interface prediction accuracy.
Integrating predicted interfaces enhances the efficiency and accuracy of protein docking.
The developed methods provide valuable tools for studying protein-protein interactions and complex structures.