From Rost Lab Open


profisis is a machine learning-based method that identifies interacting residues from sequence alone. Although the method is developed using transient protein–protein interfaces from complexes of experimentally known 3D structures, it never explicitly uses 3D infor- mation. Instead, we combine predicted structural features with evolutionary information. The strongest predictions of the method reached over 90% accuracy in a cross-validation experiment. Our results suggest that despite the significant diversity in the nature of protein–protein interactions, they all share common basic principles and that these principles are identifiable from sequence alone.

Availability/Web server

This program can be run via the PredictProtein service.

Installation with aptitude (Debian, Ubuntu, etc.)

Software Installation

Please follow this guide and install the 'profisis' package.

Generating Input Files for profisis

profisis can take an alignment profile file as an input:

  • filtered_hssp_file - PSI-BLAST alignment profile file.

Generating an HSSP Input File

Here is a protocol for converting an alignment to an HSSP profile.

Running PROFisis

Please see the PROFisis man page:

 man profisis


InteractionSites: interaction sites identified from sequence, Yanay Ofran and Burkhard Rost. Bioinformatics, Vol. 23 ECCB 2006, pages e13-e16