MPdocking I_sc

[Anonymous]

Hi guys…

I’m run the protocol MPDocking, and the result I had from the I_sc was confused.

I read here (https://www.rosettacommons.org/content/score-use-picking-top-docking-solutions) a good score is between -5 and -10, but the number is very high.

SCORE: total_score       score         rms        I_sc     cen_rms     hs_pair interchain_contact interchain_env interchain_pair interchain_vdw       mp_cbeta         mp_env        mp_pair           rama         rsigma          sheet        ss_pair        st_rmsd           time description 

SCORE:    -743.926    -743.926      20.192    -350.256      20.192       0.000              2.400          0.777           0.000          0.000       -361.705       -267.101       -117.438         -0.859          0.000          0.000          0.000         13.772        318.000 all_0001Giro_90_05005

SCORE:    -743.830    -743.831      26.179    -350.161      26.179       0.000              2.400          0.777           0.000          0.000       -361.802       -266.494       -117.852         -0.859          0.000          0.000          0.000         10.103        318.000 all_0001Giro_90_10843

SCORE:    -744.565    -744.565      23.005    -350.895      23.005       0.000              2.400          0.777           0.000          0.000       -361.802       -266.141       -118.940         -0.859          0.000          0.000          0.000         26.046        319.000 all_0001Giro_90_07090

SCORE:    -744.939    -744.939      18.740    -351.269      18.740       0.000              2.400          0.777           0.000          0.000       -361.802       -265.343       -120.111         -0.859          0.000          0.000          0.000         17.048        324.000 all_0001Giro_90_07924

SCORE:    -745.223    -745.223      14.478    -351.553      14.478       0.000              2.400          0.777           0.000          0.000       -361.592       -265.806       -120.142         -0.859          0.000          0.000          0.000         10.479        324.000 all_0001Giro_90_02086

SCORE:    -743.657    -743.657      16.201    -349.987      16.201       0.000              2.400          0.777           0.000          0.000       -361.667       -264.203       -120.104         -0.859          0.000          0.000          0.000         14.327        326.000 all_0001Giro_90_03337

SCORE:    -744.412    -744.412      18.303    -350.742      18.303       0.000              2.400          0.777           0.000          0.000       -361.802       -264.243       -120.684         -0.859          0.000          0.000          0.000         11.606        324.000 all_0001Giro_90_13761

SCORE:    -742.979    -742.979      23.599    -349.309      23.599       0.000              2.400          0.777           0.000          0.000       -361.802       -262.642       -120.852         -0.859          0.000          0.000          0.000         23.887        325.000 all_0001Giro_90_06256

 

That is correct?

[Anonymous]

The typical range of interface scores depends highly on what sorts of interfaces you’re docking (as well as the scoring function you’re using).

The -5 and -10 number you point to is for soluble protein-protein interactions, particularly for transitory complexes. (That is, for protein binding partners who are normally soluble monomers, and only come together under certain conditions.) If you’re using MPDocking, you’re in a slightly different regime, particularly if you have a complex which is an obligatory dimer (that is, the two monomers are almost always bound in the cell). — Unfortunately, I’m not familiar enough with MPDocking  to know what range is normally expected.

Another reason possible for the very favorable score you’re getting is if Rosetta is thinking there’s a disulfide bond across the interface. Rosetta docking doesn’t explicitly account for making/breaking disulfide bonds, so if it’s forming a disulfide bond in the bound state, you’ll get a very bad energy in the unbound state due to having a disulfide bond length that’s several hundered Angstroms long. This results in a very favorable binding energy, as you “gain” a whole bunch of energy going from the heavily disfavored unbound state to the decent bound state.

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