Protein–protein interactions are observed in various biological processes. They are important for understanding the underlying molecular mechanisms and can be potential targets for developing small-molecule regulators of such processes. Previous studies suggest that certain residues on protein–protein binding interfaces are "hot spots". As an extension to this concept, we have developed a residue-based method to identify the characteristic interaction patterns (CIPs) on protein–protein binding interfaces, in which each pattern is a cluster of four contacting residues.          [user manual]

Upload Structure Files
Protein 1:	*
Protein 2:	(either or)
Small Molecule 2:	(mol2 format)
Optional Parameters
Step 1: Generate Interaction pairs	Å distance_cutoff
	Å HB_dist_cutoff
	°HB_angle_cutoff
Step 2: Generate CIPs	Pattern Generation Method: pat (Feature point definition) mc (Centroid)
Step 3: Output Result	Methods of Prediction: Both hotspot and CIP Hotspot CIP
Notes: You can only assign either protein2 or small molecule 2, not both of them. Hotspot and CIP prediction is not available in fragment mode. In hotspot prediction method, residue is set to be positive when P value >= 0.5, and in CIP prediction method, pattern is set to be positive when score >=30. We calculate all resulting potential patterns in default, this takes only about 1~3 minutes.
Reference: Yan Li, Zhihai Liu, Li Han, Chengke Li, Renxiao Wang *, "Mining the Characteristic Interaction Patterns on Protein–Protein Binding Interfaces", J. Chem. Inf. Model., 2013, Vol. 53 (9), pp 2437-2447