TL;DR
The interface prediction program WHISCY is presented, which combines surface conservation and structural information to predict protein–protein interfaces and demonstrates the potential of using interface predictions to drive protein–protein docking.
The flexible data-driven docking method HADDOCK is able to predict many of the specific DNA conformational changes required to assemble the interface(s) and is the first to readily dock multiple molecules simultaneously, pushing the limits of what is currently achievable in the field of protein–DNA docking.
Analysis of subsequent use in docking highlights that Fpocket and CAVIAR are the best performing cavity prediction tools in this context and accurate binding site input does not guarantee accurate binding pose predictions and the more restrained the input is, the more reliable the docking results are.
The aim of the work is to create a lightweight desktop application for local analysis and visualization of intermolecular interactions in protein-ligand complexes using the DockAnalyzer graphical interface and the modular architecture makes expanded functionality possible.
COACH-D 2.0 is introduced, a substantially enhanced template-based method for predicting protein-ligand binding sites and features three key advances: integration of multimeric templates from Q-BioLiP into the authors' in-house library, a new multimeric structure processing module enabling binding site prediction for p...
A combined protocol in which residual dipolar couplings are first introduced as intervector projection angle restraints and at a later stage as direct restraints is shown here to give the best performance.
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