Int. J. Mol. Sci., Volume 20, Issue 13 (July-1 2019) – 263 articles
Cover Story (view full-size image):
In this work, we present GPathFinder—a novel software that determines ligand-binding pathways in proteins based on docking procedures. The method combines full atom representation for both ligands and receptors with different levels of structural flexibility. Achieving a middle ground between cavity search algorithms and extensive MD simulations, GPathFinder provides the potential pathways for a ligand to reach its binding site. The artwork illustrates how, despite the fact that all roads lead to the golden pyramid (the binding site), the journey can be more or less comfortable depending on the chosen route. View this paper.
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