Chandrajit Bajaj



F2Dock, a rigid-body protein-protein docking software, have been implemented in a client-server framework. The client is a part of the TexMol package. The client communicates with the server using XmlRPC. The server is currently installed on a computing cluster named Prism2. For a description of the algorithm, brief overview of the performance and a list of corresponding publications, refer to the Protein-protein docking project page.

  • Supported operations
    • Protein-protein docking
    • Reranking docking results
    • Protonation and partial charge assignment using PDB2PQR
    • Molecular surface generation using Molsulf
    • Separation (or addition) of skin atoms of proteins
    • Integration point sampling on the surface for energetics computaions


C. Bajaj, R. Chowdhury, and V. Siddavanahalli
F2Dock: Fast Fourier Protein-Protein Docking
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(1):45-58, 2011. (pdf)

  • Please visit for instructions on installing and using the F2DockClient
  • The source code for the F2DockServer is available upon request