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Updated: Jul 12, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Protein-protein docking: progress in CAPRI rounds 6-12 using a combination of methods: the introduction of steered
Alexander Heifetz1, Sandeep Pal, Graham R Smith
1Protein-Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne NE1 4EE, United Kingdom.
Abstract:
In recent rounds of CAPRI, the Bii group has employed a combination of techniques for the prediction of the structure of protein-protein complexes. We currently use third-party software for rigid-body and semiflexible docking (MolFit, 3D-Dock, RosettaDock), and our own steered molecular dynamics (SMD) technique for flexible refinement. SMD has also been found to be useful for discriminating near-native from false positive docking decoys. In addition to this, a variety of sources of information, including multiple descriptors of interface quality combined with a QSAR-like technique, published biological information, and continuum electrostatics calculations, are also used in the assessment of candidate complexes. We shall concentrate on results for CAPRI rounds 9-11 (targets 24-27). In these rounds, the Bii group has been successful in submitting a medium quality model for each of CAPRI targets 25 and 26, and a model of acceptable quality for target 27.
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