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PaDEL-Descriptor is a GUI for calculating molecular descriptors and fingerprints. The software currently calculates 856 descriptors (722 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints. The descriptors and fingerprints are calculated using the Chemistry Development Kit with some additional descriptors and fingerprints. These additions include atom type electrotopological state descriptors, extended topochemical atom (ETA) descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, and binary fingerprints and count of chemical substructures identified by Klekota and Roth.