Paper in Proteins: Structure, Function and Bioinformatics
A new paper is out in Proteins: from work which was presented by Ben Irwin when he visited the Pasteur Institute late last year. The paper uses hydration sites to validate the most probable binding pose of two proteins from an ensemble of binding poses. The abstract of the paper is:
We have performed docking simulations on GABARAP interacting with the GABA type A receptor using SwarmDock. We have also used a novel method to study hydration sites on the surface of these two proteins; this method identifies regions around proteins where desolvation is relatively easy, and these are possible locations where proteins can bind each other. There is a high degree of consistency between the predictions of these two methods. Moreover, we have also identified binding sites on GABARAP for other proteins, and listed possible binding sites for as yet unknown proteins on both GABARAP and the GABA type A receptor intracellular domain.