Method at a Glance

     FMAPB2 implements FMAP, a method based on fast Fourier transform (FFT), to calculate second virial coefficients (B2) for proteins represented at the all-atom level in implicit solvent. FMAP stands for FFT-based Modeling of Atomistic Protein-protein interactions. In FMAPB2, we express terms of the protein-protein inteaction energy as correlation functions, and evaluate them by FFT. These terms include steric repulsion, nonpolar attraction (in the form of a Lennard-Jones potential), and electrostatic interactions (in the form of a Debye-Hückel potential).
     FMAPB2 has been tested on lysozyme and other proteins ranging in molecular weight from 6.5 to 65 kD, over wide ranges of solvent conditions (salt concentration, pH, and temperature).
     The input to FMAPB2 is the structure of the protein, in PQR format. The user also sets the solvent condition, including ionic strength and temperature. The server will return the predicted second virial coefficient.




  • Type a name for referencing your submission
  • Enter an email address for receiving a link to the prediction by e-mail:

    • The structure file below should be in PQR format (see explanation).
    Don't know how to generate the PQR file? You can also start from PDB file

  • Upload your structure file in PQR format


  • Ionic strength for B2 calculation: (M)
  • Temperature for B2 calculation: (℃)

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