Method at a Glance

     TransComp implements the transient-complex theory for predicting protein-protein and protein-RNA association rate constants. During association, two subunits first approach each other via diffusion to form a transient complex, in which they have near-native separation and relative orientation but have yet to form the specific short-range interactions of the native complex. From there conformational rearrangement leads to the native complex. The theory predicts the association rate constant as ka = ka0 exp(-ΔGel*/kBT), where ka0 is the basal rate constant for reaching the transient complex by random diffusion, and ΔGel* is the electrostatic interaction free energy of the transient complex. When ΔGel* is very negative, a moderation factor [1 + 10-4 exp(-ΔGel*/kBT)]-1 is applied to correct for overestimation of ka.
     The theory so far works for cases where association is limited by diffusion (as opposed to by conformational rearrangement). These cases are signified by small conformational changes upon association and by rate constants that are greater than ~104 M-1s-1.
     The input to TransComp is the structure of the native complex, in PQR format, with separate files for the two subunits. The server will return the predicted association rate constant. Or, if your system falls outside the domain of its applicability, TransComp will so indicate and return a null result. That usually means that the association of your system is more complicated than rigid-body docking and involves multiple steps.

If you have more than a few protein complexes and would like to run TransComp on your own computer, click Download.

  • Type a name for referencing your submission
  • Enter an email address if you also want to receive a link to the prediction by e-mail; otherwise leave it blank:

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

  • Upload your structure file for the first subunit in PQR format

  • Upload your structure file for the second subunit in PQR format

  • Ionic strength for ka calculation: (M)

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