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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...

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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.
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Ligand Binding Sites

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.
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Related Experiment Video

Updated: Dec 24, 2025

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

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

Published on: January 26, 2024

ProteinsPlus: interactive analysis of protein-ligand binding interfaces.

Katrin Schöning-Stierand¹, Konrad Diedrich¹, Rainer Fährrolfes¹

¹Universität Hamburg, ZBH - Center for Bioinformatics (ZBH), 20146 Hamburg, Germany.

Nucleic Acids Research

|April 17, 2020

Summary

This summary is machine-generated.

ProteinsPlus is a web service that helps scientists analyze protein structures and interactions. It now features keyword search and new tools for ligand validation, water molecule placement, and metal ion coordination, plus a REST service for automation.

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Published on: July 14, 2015

Area of Science:

Structural biology
Biochemistry
Bioinformatics

Background:

Publicly available protein structure data is rapidly increasing, presenting challenges in searching and analysis.
Existing tools require specific knowledge of Protein Data Bank (PDB) codes for structure retrieval.
Efficiently investigating protein-ligand interactions is crucial for drug discovery and biological research.

Purpose of the Study:

To enhance the ProteinsPlus web service for easier access to protein structure analysis tools.
To introduce new functionalities for improved protein-ligand interaction studies.
To enable automated integration of protein structure analysis into computational pipelines.

Main Methods:

Development of a web interface with intuitive access to a suite of protein analysis tools.
Implementation of a keyword search functionality on the ProteinsPlus homepage.
Augmentation of the tool collection with StructureProfiler, WarPP, and METALizer.
Provision of a REST service for programmatic access to all tools.

Main Results:

ProteinsPlus now offers keyword-based structure searching, eliminating the need for PDB codes.
New tools enable validation of ligands and active sites (StructureProfiler), placement of water molecules (WarPP), and analysis of metal ion coordination (METALizer).
The service has undergone infrastructural improvements and provides a REST API for automated workflows.

Conclusions:

The enhanced ProteinsPlus web service provides a more accessible and comprehensive platform for protein structure analysis.
The new tools and features cater to a wider range of user needs in life sciences and computational biology.
The availability of a REST service facilitates the integration of ProteinsPlus into automated structure processing and modeling pipelines.