Our Software

Computer-aided drug design platform using PyMOL This software package contains three Python plugins for PyMOL that facilitate performing molecular mechanics applications (using AMBER), docking simulations (using AutoDock Vina and SLIDE) and combinations of both (e.g. ensemble docking). Download software
Docking suite based on optimized protein pharmacophore models This software package contains the docking program PharmDock and a plugin to interface with PyMOL. Download software
Hydration site analysis program WATsite This software package contains the hydration site analysis program WATsite together with an easy-to-use graphical user interface based on PyMOL which elucidates the thermodynamic profile of individual water molecules and their potential contribution to ligand binding. Download software
Quasi-three body statistical potential using functional groups Distance-based statistical potentials have long been used to model condensed matter systems e.g. as scoring functions in differentiating native-like protein structures from decoys. We have extended distance-dependent pair-wise atomistic statistical potentials to corresponding interaction functions that are conditional on a third interacting body, defined as quasi-three-body statistical potentials. The following data files contain quasi-three body statistical potentials using a representation of the protein based on physico-chemical properties (A=hydrogen-bond acceptor; D=hydrogen-bond donor; H=hydrophobic; N=formally negative; P=formally positive; R=aromatic element). The potentials were derived from a statistical analysis of a large subset of the PDB databank. Download data files