Figure 1

Surface points used in geometric hashing. A, Example of surface points. Surface points of 1A2K chain B (left, purple, 248 residues) are colored in blue for non-PPI surface (1652 points) and yellow for the PPI region (25 residues, 248 points). Critical points of 1A2K chain C (right, yellow, 196 residues) are colored in green for non-PPI surface (1332 points) and red for the PPI region (16 residues, 165 points). B, Two schemes for restricting docking interface using predicted PPI regions in geometric hashing. Two base points are selected from points that locate within the predicted PPI regions (gray ellipsoid). Given the two base points (crosses), points in their neighborhood (within 15Å; showed in two circles) are transformed based on the coordinate system defined by the base points, which are then stored in a hash table. Fitness of local regions around the base points of the ligand and the receptor proteins are evaluated by the number of equivalent matching points (the voting stage). In a permissive search, points from outside of the PPI region (squares) as well as points within the PPI region (triangles) are considered. For a restrictive search, only the points in the PPI region (triangles) are considered.