Research question
Can an electron-density representation improve binding-affinity prediction when atomic coordinates are uncertain?
How the method works
E-CloudBind combines covalent molecular graphs with point clouds representing ligand electron density and a protein-pocket density proxy. Ligand densities are approximated with GFN2-xTB; pocket clouds use van der Waals-guided Gaussian functions. A heterogeneous graph network combines these features to predict binding affinity.