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FireDock Scoring Parameters

Name attrVdWWeight repVdWWeight ACEWeight attrElWeight repElWeight l attrElWeight l repElWeight HBWeight pipiWeight catpiWeight aliphWeight insidenessWeight confProbWeight

Enzyme/Inhibitor coarse full 1 1 0.95 0 1.6 1.6 0.07 0.07 0.12 0.12 0 0 0.3 0.3 1.32 1.32 1 1 0.8 0.8 0.5 0.5 1.55 1.55 0 0

Antibody/Antigen coarse full 1.5 1.5 0.6 0.1 1.6 1.6 0.21 0.21 0.21 0.21 0.46 0.46 0.69 0.69 1.2 1.2 1 1 0.7 0.7 2.5 2.5 0 0 0 0

Others coarse 1.5 0.8 1.6 0.21 0.21 0 0.69 1.2 1 0.7 2.5 0.7 0

full 1.5 0 1.6 0.21 0.21 0 0.69 1.2 1 0.7 2.5 0.7 0

Table 1: Program parameters for score calculation for different complex types. Parameters are specified for the full and coarse refinement stages. The parameters described in the table are weights of the following scoring terms: • attrV dW W eight - softened attractive van der Waals interactions • repV dW W eight - softened repulsive van der Waals interactions • attrElW eight - attractive short-range Coulomb electrostatics • repElW eight - repulsive short-range Coulomb electrostatics • l attrElW eight - attractive long-range Coulomb electrostatics • l repElW eight - repulsive long-range Coulomb electrostatics • ACEW eight - Atomic Contact Energy (ACE) potential • HBW eight - hydrogen and disulfide Bonds • catpiW eight - cation-π stacking • pipiW eight - π-π stacking • aliphW eight - aliphatic interactions • insidenessW eight - “insideness” measure • conf P robW eight - internal energy

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