Get   for     ? 
 Site search     ? 
CAPRI: Critical Assessment of PRediction of Interactions
 
  
   Call For Targets
   Meeting Report
   Evaluation Meeting
Registration
   Evaluation Meeting
Program
   ROUND 1
   ROUND 2
 
 MSD  CAPRI: Critical Assessment of PRediction of Interactions

First community wide experiment on the comparative evaluation of protein-protein docking for structure prediction

Hosted By EMBL/EBI-MSD Group

CAPRI Target07 evaluation results

Raúl Méndez, Raphaël Leplae and Shoshana J. Wodak.
SCMBB Université Libre de Bruxelles, Cp 263, Brussels, Belgium.
Re-accessed on Monday December 16, 2002.
e-mail: raul@ucmb.ulb.ac.be
shosh@ucmb.ulb.ac.be

The evaluation results of the CAPRI target 07 predictions are stored in different directories depending on the criteria that have been used. In the following the directories and their contents are briefly described.


Information.

Directory Information contains the information about target 07, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_07_xray.pdb: the crystal structure of the target (target 07) in PDB format: Streptococcal pyrogenic exotoxin A complex T cell receptor beta chain.
  • Contres: list of residue contacts in the target between T cell receptor beta chain subunit R and Streptococcal pyrogenic exotoxin A subunit A.
  • capri.07.R.intres: T cell receptor beta chain - Streptococcal pyrogenic exotoxin A interface residues.
  • cc.capri.07.R.d: list of clashes in the target interface.
    Final Summary

    File target 07 Final Summary. summarizes all the information about the target 07 evaluation in the same way as the corresponding summary file for target 01. It looks like that:

    
    
    PREDS			fnat		fnon-nat		 		fIR		 	INTERFACE RES.(OP)		THETA ANGLE	DISTANCE	Nclash		L_rmsd		I_rmsd
    								   Antibody  	Antigen   	   Antibody  	Antigen   
    
    T07_P01.1.R 0.811 0.211 0.952 0.824 0.909 0.824 7.2 1.307 12 2.122 0.912 T07_P01.2.R 0.162 0.870 0.714 0.706 0.600 0.667 62.0 5.409 32 11.388 4.807 T07_P01.3.R 0.000 1.000 0.857 0.176 0.692 0.091 126.3 30.109 20 35.402 12.996 T07_P01.4.R 0.000 1.000 0.571 0.000 0.632 0.000 101.4 38.093 26 40.510 9.326 T07_P01.5.R 0.000 1.000 0.905 0.000 0.760 0.000 130.2 49.437 31 53.170 13.339
    .
    .

    Again T07_P01.1.R means participant 01, prediction 1 for the target 07, antibody interface R. Participant 02 named the corresponding T cell chain H.

    Column 2 gives the fraction of predicted contacts over native fnat. This fraction is computed as the number of contacts in the prediction that match the contacts in the target, divided by the number of contacts in the target. As for target 01, 2 residues are considered as being in contact if at least one atom of one residue is within 5Å of an atoms of the other.

    Colum 3 gives the non-native fnon-nat contact fraction. This fraction is computed as the number of contacts in the prediction that don't match the contacts in the target, divided by the number of contacts in the prediction. This number accounts for the real efficiency of the prediction in term of contact: as bigger is the predicted interface as higher the probability of predict native contacts.

    Columns 4 and 5 list the interface residues ratios over native fIR. Column 4 give the ratio between the residues of the T cell receptor that are part of the interface in the prediction, over the T cell receptor residues that are part of the interface in the target. The 5th column gives the same information for the Streptococcal pyrogenic exotoxin A moiety. All the interface residues lists are generated using the BRUGEL package.

    Columns 6 and 7 lists the interface residue ratios over prediction. They are analogous to columns 4 and 5 but now dividing the number of residues in the prediction found in the target over the total number of provided residues at the predicted interface.

    Column 8 lists the rotation angle (Theta angle) necessary to fit the T cell receptor molecule in the predicted complex to that in the target, as per capri_07_xray.pdb. To compute this angle, we first perform a rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) of the Streptococcal pyrogenic exotoxin A subunit in the predicted complex, to the Streptococcal pyrogenic exotoxin A subunit in the target.

    After this first fit, a second fit is performed so as to superimpose the predicted T cell receptor molecules onto its closest counterpart in the target structure (capri_04_xray.pdb closest). The rotation angle corresponding to this second fitting is the listed theta angle. Due to the conformational changes on the T cell receptor upon binding, we consider for the superimposition to the variable domain on the T cell receptor (residues from 3 - 118).

    Column 9 lists the distance (in Angstroms) between geometric centers of predicted and target T cell receptor molecules before the second fit. The distance between the geometric centers together with the Theta angle give an idea of the global position of the T cell receptor in the prediction relative to the position in the target.

    Column 10 lists the number of clashes Nclash between the T cell receptor and the Streptococcal pyrogenic exotoxin As for each predicted complex. Clashes are computed between heavy atoms within 3 Å . In the detailed information you can find the close contact pairs classified into three categories: from 0 to 1, from 1 to 2 and from 2 to 3 Å.

    Columns 11 and 12 list the RMSD's (Root Mean Square Deviation) values in Å . Column 11 list the RMSD values calculated between the T cell receptor's backbones once the Streptococcal pyrogenic exotoxin As are superimposed. Column 12 contain the rsmd's when sumperimposing the backbones of the residues at the interface (T cell receptor + Streptococcal pyrogenic exotoxin A) on the prediction upon the counterpart in the target I_rmsd. Residues at the interface are re-defined here, as residues in the target having at least one atom within 10 Å of an atom of the other molecule. The equivalents for those residues in the predictions are considered as to be in the interface to sumperimpose. For all the RMSD calculations we consider the same molecular fragments as for the fits.


    Contact List

    Directory: ContactList contains one file per predicted interface, with information on the residue-residue contacts in the predicted versus the target complexes

    As an example the file T07_P01.1.R.highlighted is illustrated in part:

    HIGHLIGTHED CONTACT LIST FOR T07_P01.1.R
    Number of Contacts = 38 Matching List1 = 30/37



    R27   ASN - A94   GLU
    R28   ASN - A94   GLU 1
    R28   ASN - A95   ARG
    R30   ASN - A84   TYR
    R50   TYR - A85   HIS 1
    
    .
    .

    Each predicted contact that matches the target contact list is highlighted with a number indicating the reference list is matching. For this round "1" refers to the only possible list. Names and numbering of residues listed in these files are corrected according to the target ones.


    INTERFACE_RESIDUES_HIGHLIGHTED

    Directory InterfaceResidues contains one file per predicted interface, with information on the residues forming the Streptococcal pyrogenic exotoxin A - T Cell receptor interface in the prediction and how well they match those in the target interfaces.

    The information contained in each file is illustrated by an example, T07_P01.1.R.highlighted

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T07_P01.1.R
    N_res_Antibody = 22 N_res_Antigen = 17 Match Antibody in List1 = 20/21 Matching Antigen in List1 = 14/17


    T CELL RECEPTOR LIST
    
    R27   ASN    3.813
    R28   ASN   84.558 1
    R30   ASN   28.216 1
    R31   ASN    0.816
    R47   HIS    0.127 1
    
    .
    . STREPTOCOCCAL PYROGENIC EXOTOXIN A1 LIST A15 VAL 0.095 A16 LYS 9.731 1 A17 ASN 60.238 1 A19 GLN 36.909 1
    .
    .

    Each time a residue of the T Cell receptor or Exotoxin A in the predicted interface matches one of the interface residues in the target list, it is highlighted with the number of the corresponding target reference list, 1 again stands for the number of the unique list.

    Note that interface residues list files and contact list ones are named the same (i.e. T07_P01.1.R.highlighted) but they are in different directories and their contents are completely different. Names and numbering of residues listed in these files are corrected according to the target ones.


    FITTING_SUMMARY

    Directory FittingSummary contains one file per predicted interface, with information on the results of fitting the predicted complex over the target complex. The information contained in each file is illustrated by an example, file T07_P01.1.R.fitting.summary

    Fitting of A prediction Antigen Subunit onto B CAPRI Antigen Subunit
    Rotation Matrix:
       0.59626  -0.25859  -0.76000
      -0.46023   0.66558  -0.58754
       0.65777   0.70010   0.27785
      Translation vector     42.215   -28.630    44.958
    Fitting Antibodies, R onto G
    Theta angle = 7.25
    Distance between geometric centres = 1.307124
    

    As for the evaluation of target 01, we give the information about the first fit (rotation matrix and translation vector including which subunits are involved), the distance between predicted antibody and Capri antibody after this first fit (considering just the fragment that is fitted in the second fit) and the Theta angle of the second fit.

    For this target 07 evaluation, the first fit was made using the backbones of the common longest fragment Streptococcal pyrogenic exotoxin A subunit, residues 3-219 while the second fit was made considering only the the variable domain on the T cell receptors, residues 3-118. In order to be consistent, the distance between geometric centres was calculated taking into account only these antibody fragments.

    Note that in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri_07_xray.pdb) were renamed as follows:

    A to B
    for the Streptococcal pyrogenic exotoxin A subunit
    R (or H for P02) to G
    for the T Cell Receptor subunit.


    FITTING_SUMMARY FITTED PDB

    Directory FittedPDB contains the files with the coordinates of the predicted and target complexes superimposed, following the first fit, in which the Streptococcal pyrogenic exotoxin A subunits have been superimposed (using the listed rotation matrix and translation vector).

    Fitted pdb files are regenerated now using the new transformations.


    CLOSE_CONTACTS

    Directory CloseContacts contains one file per predicted interface with information on the clashes in each predicted interface.

    For example part of file cc.T07_P01.1.R.d looks like that:

    T CELL RECEPTOR Atom    EXOTOXIN A1 Atom   Distance
    
    --
    R 56   .GLU.OE1     A 17   .ASN.ND2         2.29
    R 28   .ASN.ND2     A 94   .GLU.CB          2.31
    R 55   .THR.O       A 20   .ASN.OD1         2.44
    R 28   .ASN.ND2     A 94   .GLU.CD          2.45
    R 53   .GLY.O       A 23   .PHE.CB          2.46
    R 28   .ASN.ND2     A 94   .GLU.CG          2.48
    R 28   .ASN.ND2     A 94   .GLU.OE1         2.49
    R 72   .GLN.N       A 54   .ASN.OD1         2.85
    R 55   .THR.OG1     A 19   .GLN.OE1         2.86
    R 55   .THR.O       A 19   .GLN.OE1         2.95
    R 67   .ALA.O       A 162  .ASN.ND2         2.97
    R 56   .GLU.OE2     A 20   .ASN.ND2         3.00
    

    As in the evaluation of target 01, the list of clashes is segregated into contacts between 0-1, 1-2 (no contacts for these two blocks in the example above) and 2-3Å. Residue names and numbering here correspond to the original ones.