A generalized statistical scoring potential is used to account for varying chemical environments, such as metal ions, cofactors, water molecules, etc. The scoring function employed by the CANDOCK algorithm is a pairwise atomic scoring function that is based on the work carried out by Bernard and Samudrala . Here we reproduce the fundamental equations developed in Ref. 26 to clarify the terminology used in the present work. The scoring function calculates the potential between two atoms based on the distance between atoms i and j with atom types a and b and takes four input terms that determine the method by which score is calculated. The possible terms are 'functional', 'reference', 'composition', and 'cutoff'. They define the function P given in the basic Eq. ( ):