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 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 target 04 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 04 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 04, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_04_xray.pdb: the crystal structure of the target (target 04) in PDB format: Pig Alpha-Amylase complex camelide antibody VH domain 1.
  • Contres: list of residue contacts in the target between antibody VH subunit H and Alpha-Amylase subunit A.
  • capri.04.H.intres: antibody VH - Alpha-Amylase interface residues.
  • cc.capri.04.H.d: list of clashes in the target interface.
    Final Summary

    File target 04 Final Summary summarizes all the information about the target 04 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   
    
    T04_P01.1.H 0.000 1.000 0.630 0.027 0.680 0.023 117.0 48.225 46 52.415 18.504 T04_P01.2.H 0.000 1.000 0.407 0.054 0.611 0.067 101.9 37.422 18 40.350 12.692 T04_P01.3.H 0.000 1.000 0.556 0.000 0.517 0.000 158.1 48.551 43 53.711 19.606 T04_P01.4.H 0.000 1.000 0.333 0.000 0.409 0.000 179.2 51.948 30 56.570 18.578 T04_P01.5.H 0.000 1.000 0.519 0.000 0.737 0.000 166.6 66.213 9 69.726 20.502
    .
    .

    Column 1 lists the prediction identifier (i.e. T04_P01.1.A means participant 01, prediction 1 for the target 4, using Camelid Antibody chain A in the unbound coordinates)

    Column 2 gives the fraction of predicted contacts over native. 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 fraction of predicted contacts over prediction. 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 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. Column 4 give the ratio between the residues of the Camelid Antibody that are part of the interface in the prediction, over the Camelid Antibody residues that are part of the interface in the target. The 5th column gives the same information for the Alpha-amylase 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 Camelid Antibody molecule in the predicted complex to that in the target, as per capri_04_xray.pdb. To compute this angle, we first perform a rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) of the Alpha-amylase subunit in the predicted complex, to the Alpha-amylase subunit in the target.

    After this first fit, a second fit is performed so as to superimpose the predicted Camelid Antibody 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.

    Column 9 lists the distance (in Angstroms) between geometric centers of predicted and target Camelid Antibody 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 Camelid Antibody in the prediction relative to the position in the target.

    Column 10 lists the number of clashes Nclash between the Camelid Antibody and the Alpha-amylases for each predicted complex. Clashes are computed between heavy atoms within 3 Å . In the detailed information you can find the clash 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 Camelid Antibody's backbones once the Alpha-amylases are superimposed. Column 12 contain the rsmd's when sumperimposing the backbones of the residues at the interface (Camelid Antibody + Alpha-amylase) on the prediction upon the counterpart in the target. 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.

  • target 04, final summary of the complementary analysis. The complementary analysis consists in comparing the predictions not only to target 04, but also to targets 05 and 06, and listing the results for the predictions with the best score overall. This multiple comparison increases the chances for getting a better score for your predictions. For further details, please consult the CAPRI round 2 documentation (Numerical evaluation). This file looks like that:
    PREDICTION             CONTACTS         INTERFACE RES.        THETA ANGLE       DISTANCE    
    
    T04_P01.1.A.D 1/65 8/29 23/37 141.10 10.014 T04_P01.2.A.D 1/65 12/29 17/37 80.20 26.831 T04_P01.3.A.D 1/65 19/29 22/37 101.40 3.172
    .
    .

    In this table suffix A.B indicates the evaluation with respect to target 04, suffix A.C refers to with respect to target 05 and A.D refers to the evaluation with 06 (the one with the standard antibody binding mode).

    Now by clicking on any prediction label, the structure for the given prediction together with the targets 04, 05 and 06 fitting all four antigens is displayed. In fact the displayed structures are contained in the corresponding *.3_target.pdb files (see FittedPdb section for details).


    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 T04_P06.2.H.highlighted is illustrated in part:

    HIGHLIGTHED CONTACT LIST FOR T04_P06.2.H
    Number of Contacts = 36 Matching List1 = 1/58



    H51   ILE - A173  ASP
    H54   ASP - A212  ASP 1
    H54   ASP - A213  LYS
    H55   GLY - A177  SER
    

    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.

  • The ContactList directory also contains the analogous files for the multiple comparison of any predicted contact list for target 04 versus any contact list from target 04, 05 or 06, highlighting residues that match each target contact list. The equivalence between residues from the different antibodies (H chains) was deduced from the corresponding ClustalX multiple sequence alignment capri_456_xray_H.jpg.

    As an example the file T04_P16.4.H.complementary_highlighted is partially shown:

    HIGHLIGTHED CONTACT LIST FOR T04_P16.4.H

    Number of Contacts = 130 Matching List_T04_1 = 0/58 Matching List_T05_1 = 0/64 Matching List_T06_1 = 11/65



    .
    .
    . H54 ASP - A105 SER T06_1 H54 ASP - A106 GLY T06_1 H54 ASP - A124 ARG H54 ASP - A145 SER H54 ASP - A161 GLN H55 GLY - A106 GLY T06_1 H71 GLN - A106 GLY
    .
    .
    .

    In this file we have the different contact ratios which depend on the target with which the comparison is made (see the header), and the corresponding matching contacts highlighted, this time with the name of the target list it matches. In the example T06_1 stands for target 06 list 1 (as there is only just one list for targets 04, 05 and 06).


    INTERFACE_RESIDUES_HIGHLIGHTED

    Directory InterfaceResidues contains one file per predicted interface, with information on the residues forming the Alpha-Amylase - VH antibody 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, T04_P06.2.H.highlighted

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T04_P06.2.H
    N_res_Antibody = 18 N_res_Antigen = 19 Match Antibody in List1 = 7/27 Matching Antigen in List1 = 1/37


    AMYD10 VHH LIST
    
    H51   ILE    3.507
    H52   ASP    0.534 1
    H54   ASP   34.204 1
    H55   GLY   29.692
    H56   THR   58.205 1
    H57   THR   59.096 1
    H58   THR    0.665 1
    
    .
    . PIG ALPHA-AMYLASE LIST A127 PRO 5.493 A128 ALA 0.229 A129 VAL 4.152 A130 PRO 56.266
    .
    .

    Each time a residue of the VH antibody or Alpha-amylase 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 the files for the interface residue list and the contact list have the same name (i.e. T04_P06.2.H.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.

  • The same InterfaceResidues directory, also contains the corresponding files for the multiple comparison. As in the ContactList section, the equivalence between residues from the three different antibodies (H chains) is based on the same ClustalX multiple sequence alignment capri_456_xray_H.jpg.

    As an example the file T04_P16.4.H.complementary_highlighted is partially shown:

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T04_P16.4.H
    N_res_Antibody = 35 N_res_Antigen = 49 Matching Antibody in List_T04_1 = 8/27 Matching Antigen in List_T04_1 = 1/37 Matching Antibody in List_T05_1 = 6/29 Matching Antigen in List_T05_1 = 1/25 Matching Antibody in List_T06_1 = 18/29 Matching Antigen in List_T06_1 = 33/37


    AMYD10 VHH LIST
    
    H2    VAL   65.797 T06_1
    H3    GLN   96.840
    
    .
    .
    . PIG ALPHA-AMYLASE LIST A49 VAL 0.007 A50 VAL 9.404 A51 VAL 20.108 T06_1
    .
    .
    .

    In this files we extended the comparisons done on *.highlighted files against targets 04, 05 and 06. Now as before, the matching target list for any residue either in the Antibody moeity or in the Antigen's is indicated.


    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 T04_P06.2.H.fitting.summary

    Fitting of A prediction Antigen Subunit onto B CAPRI Antigen Subunit
    Rotation Matrix:
      -0.13942  -0.94535  -0.29475
      -0.57913  -0.16360   0.79865
      -0.80323   0.28205  -0.52467
      Translation vector    107.937    81.602    60.981
    Fitting Antibodies, H onto G
    Theta angle = 136.35
    Distance between geometric centres = 44.90052
    

    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 04 evaluation, the first fit was made using the backbones of the common longest fragment Alpha-Amylase subunit, residues 2-496 while the second fit was made considering the common longest antibody fragments to all the participants, e.g. residues 1-82; 85-102 and 108-119. 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_04_xray.pdb) were renamed as follows:

    A to B
    for the Alpha-Amylase subunit
    H to G
    for the VHH antibody subunit.

  • In the FittingSummary directory are stored the files *.fitting.complementary.summary, that are analogous to the previous ones but now also containing the parameters corresponding to the fit onto the target to which the prediction scores best in terms of contacts.

    As an example file T04_P16.4.H.J.fitting.complementary.summary:

    Fitting of A prediction Antigen Subunit onto D CAPRI Antigen Subunit
    Rotation Matrix:
      -0.13376  -0.94590  -0.29560
      -0.58113  -0.16675   0.79654
      -0.80274   0.27832  -0.52739
      Translation vector    107.813    81.841    61.158
    Fitting Antibodies, H onto J
    Theta angle = 50.94
    Distance between geometric centres = 7.213577
    

    As for the previous files, we provide the information about the first fit (rotation + translation) now related to the antigen on the target which scores the best contact ratio. The second fit, as ever, is between the antibodies after the first fit is performed related to that target that scores the best contact ratio.

    For the first fit, we use the same antigen fragment that has been used in *.fitting.summary files, while for the second fit, we define the equivalent sequence segment among different antibodies based on the basis of the ClustalX multiple sequence alignment capri_456_xray_H.jpg we mentioned above.

    Note that in order to not confuse chain ID's between different targets and predicted coordinate sets, the chain ID's on the different targets were renamed as follows:

    A to B
    for the Alpha-Amylase subunit in T04
    A to C
    for the Alpha-Amylase subunit in T05
    A to D
    for the Alpha-Amylase subunit in T06
    H to G
    for the Antibody subunit in T04
    H to I
    for the Antibody subunit in T05
    H to J
    for the Antibody subunit in T06.


    FITTED PDB

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

  • The FittedPdb directory contains now the coordinates for the first fits respectively onto T04, T05 and T06 antigens, the corresponding files are *.H.B.pdb, (identical to *.H.pdb files), *.H.C.pdb and *.H.D.pdb. The coordinate files containing all the possible fits between a given predicted antigen and the antigens in all three targets are named *.3_target.pdb files.

    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.T04_P06.2.H.d looks like that:

    AMYD10 VHH Atom    PIG ALPHA-AMYLASE Atom   Distance
    
    --
    H 65   .GLY.O       A 134  .TRP.NE1         1.80
    --
    H 64   .ALA.CB      A 130  .PRO.CG          2.04
    H 65   .GLY.N       A 174  .TYR.OH          2.43
    H 64   .ALA.CB      A 130  .PRO.CD          2.43
    H 65   .GLY.O       A 134  .TRP.CD1         2.65
    H 57   .THR.O       A 181  .ASP.OD2         2.65
    H 65   .GLY.N       A 174  .TYR.CZ          2.76
    H 57   .THR.OG1     A 177  .SER.CB          2.89
    H 65   .GLY.O       A 134  .TRP.CE2         2.91
    H 65   .GLY.C       A 134  .TRP.NE1         2.97
    

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