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Open Access Software

ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces

Rudra P Saha, Ranjit P Bahadur, Arumay Pal, Saptarshi Mandal and Pinak Chakrabarti*

Author Affiliations

Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India

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BMC Structural Biology 2006, 6:11  doi:10.1186/1472-6807-6-11

Published: 7 June 2006



Molecular recognition is all pervasive in biology. Protein molecules are involved in enzyme regulation, immune response, signal transduction, oligomer assembly, etc. Delineation of physical and chemical features of the interface formed by protein-protein association would allow us to better understand protein interaction networks on one hand, and to design molecules that can engage a given interface and thereby control protein function on the other hand.


ProFace is a suite of programs that uses a file, containing atomic coordinates of a multi-chain molecule, as input and analyzes the interface between any two or more subunits. The interface residues are shown segregated into spatial patches (if such a clustering is possible based on an input threshold distance) and/or core and rim regions. A number of physicochemical parameters defining the interface is tabulated. Among the different output files, one contains the list of interacting residues across the interface. Results can be used to infer if a particular interface belongs to a homodimeric molecule.


A web-server, ProFace (available at webcite) has been developed for dissecting protein-protein interfaces and deriving various physicochemical parameters.