Four knowledge-based scoring matrices of iMatrix. (A) Sidechain to sidechain van der Waals scoring matrix; (B) Sidechain to backbone van-der Waals scoring matrix; (C) Sidechain to sidechain special-bond scoring matrix; (D) Sidechain to backbone special-bond scoring matrix. The sidechain to sidechain scoring matrices are symmetric. For sidechain to backbone matrices, y-axis denotes side chain and x-axis denotes backbone. We discard backbone-backbone matrixes because the backbone-backbone interacting forces are constant in our template-based method.