Default parameters used for classification of protein-protein interfaces for recognition of similar spatial and chemical organizations

1. The side lengths of the matched triangles are required to be similar up to 3A.
2. The side lengths of the triangles used for matching must be more than 3A but less then 15A.
3. The distance between the matched pseudocenters must be less than 3A.
4. The difference of the values of the solid angle shape function (Connolly 1986) measured at the patch centers must be 0.4.
5. The smooth molecular surfaces (Connolly 1983) are constructed with a probe sphere of 1.4A.
6. The resolution of a Distance Transform Grid used for the calculations is  0.5A.
7. The default radius of the sphere used to calculated the solid angle shape function (Connolly 1986) is 3.5A. The final value used to represent the average curvature of each region is the average of this value and the solid angle shape function calculated in the sphere bounding the surface patch with the corresponding physico-chemical property.