Related Experiment Video
Updated: Jun 12, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Detection and refinement of encounter complexes for protein-protein docking: taking account of macromolecular
Xiaofan Li1, Iain H Moal, Paul A Bates
1Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, London WC2A 3PX, United Kindom.
Abstract:
Analysis of trajectories from our rigid-body dynamics simulation package, BioSimz, is used to find regions on the surface of unbound proteins that form frequent and tenacious encounter complexes with their binding partner. Binding partners are significantly more likely to sojourn around true binding regions than around the remainder of the protein surface. This information is used to restrict the search space for flexible protein-protein docking using our SwarmDock algorithm, reducing the computational expense of docking, and improving or matching the ranking of successfully docked poses for all but four of 26 test cases. Running the simulations with external crowder proteins, at near physiological concentration, further enhances the binding region, compared to simulations without external crowders. Information gleaned from these simulations can give mechanistic insights into binding events. The application of these techniques to CAPRI targets 32 and 38-40 is discussed.
Related Concept Videos
Protein-protein Interfaces
Protein-Protein Interfaces
Protein Complexes with Interchangeable Parts
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
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 Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Assembly of Signaling Complexes
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
