Raphael A. G. Chaleil

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Protein-protein interactions are central to almost all biological functions, and the atomic details of such interactions can yield insights into the mechanisms that underlie these functions. We present a web server that wraps and extends the SwarmDock flexible protein-protein docking algorithm. After uploading PDB files of the binding partners, the server(More)
In previous CAPRI rounds (3-5) we showed that using MD-generated ensembles, as inputs for a rigid-body docking algorithm, increased our success rate, especially for targets exhibiting substantial amounts of induced fit. In recent rounds (6-11), our cross-docking was followed by a short MD-based local refinement for the subset of solutions with the lowest(More)
Within the crowded, seemingly chaotic environment of the cell, proteins are still able to find their binding partners. This is achieved via an ensemble of trajectories, which funnel them towards their functional binding sites, the binding funnel. Here, we characterize funnel-like energy structures on the global energy landscape using time-homogeneous finite(More)
We present optimisations applied to a bespoke bio-physical molecular dynamics simulation designed to investigate chromosome condensation. Our primary focus is on domain-specific algorithmic improvements to determining short-range interaction forces between particles, as certain qualities of the simulation render traditional methods less effective. We(More)
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