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Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...

Protein Complexes with Interchangeable Parts

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Related Experiment Video

Updated: May 14, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

SwarmDock: a server for flexible protein-protein docking.

Mieczyslaw Torchala¹, Iain H Moal, Raphael A G Chaleil

¹Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK.

Bioinformatics (Oxford, England)

|January 25, 2013

Summary

We developed a web server for protein-protein docking using the SwarmDock algorithm. This tool predicts binding conformations and structures, aiding in understanding biological functions.

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Last Updated: May 14, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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Published on: July 8, 2025

Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

Protein-protein interactions are fundamental to cellular processes.
Understanding these interactions at an atomic level is crucial for deciphering biological mechanisms.

Purpose of the Study:

To present a novel web server for flexible protein-protein docking.
To extend the capabilities of the SwarmDock algorithm for predicting interaction interfaces.

Main Methods:

The web server utilizes the SwarmDock algorithm for flexible protein-protein docking.
Users upload Protein Data Bank (PDB) files of interacting proteins.
The server generates low-energy conformations and clusters docking poses.

Main Results:

The server successfully generates ranked lists of predicted protein-protein complex structures.
It allows for both global docking and targeted docking focused on specific residues.
Validation against the CAPRI experiment and docking benchmarks demonstrates high performance.

Conclusions:

The developed web server provides an effective platform for protein-protein docking.
It offers valuable insights into the atomic details of protein interactions.
The tool is a significant advancement compared to existing docking servers.