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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 05 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 05 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 05, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_05_xray.pdb: the crystal structure of the target (target 05) in PDB format: Pig Alpha-Amylase complex camelide antibody VH domain 2.
  • Contres: list of residue contacts in the target between antibody VH subunit H and Alpha-Amylase subunit A.
  • capri.05.H.intres: antibody VH - Alpha-Amylase interface residues.
  • cc.capri.05.H.d: list of clashes in the target interface.
    Final Summary

    File target 05 Final Summary. summarizes all the information about the target 05 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   
    
    T05_P01.1.H 0.000 1.000 0.517 0.000 0.682 0.000 178.3 60.762 45 64.491 18.993 T05_P01.2.H 0.000 1.000 0.517 0.000 0.789 0.000 128.6 50.750 39 54.884 20.801 T05_P01.3.H 0.000 1.000 0.759 0.000 0.786 0.000 123.3 42.230 54 45.512 13.866 T05_P01.4.H 0.000 1.000 0.483 0.000 0.778 0.000 140.3 60.997 24 64.131 18.815 T05_P01.5.H 0.000 1.000 0.552 0.000 0.615 0.000 84.8 51.949 81 54.083 19.085
    .
    .

    Again T05_P01.1.H means participant 01, prediction 1 for the target 05, antibody interface H.

    For that round 2, a maximum number of 5 prediction per participant is considered, except for participant P08 that submitted only 4 models.

    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 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_05_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_05_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 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.

  • target 05, final summary of the complementary analysis. The complementary analysis consists in comparing the predictions not only to target 05, but also to targets 04 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    
    
    T05_P01.1.A.D 0/65 11/29 0/37 145.65 74.367 T05_P01.2.A.D 2/65 9/29 23/37 100.06 9.382 T05_P01.3.A.D 0/65 9/29 2/37 108.77 46.109 T05_P01.4.A.D 0/65 7/29 0/37 156.08 74.410
    .
    .

    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 T05_P04.3.H.highlighted is illustrated in part:

    HIGHLIGTHED CONTACT LIST FOR T05_P04.3.H
    Number of Contacts = 63 Matching List1 = 7/64



    H2    VAL - A152  ASN
    H3    GLN - A152  ASN
    H91   TYR - A149  GLU
    H96   PRO - A239  GLY 1
    H97   GLY - A238  GLY 1
    H98   SER - A237  LEU 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.

  • The ContactList directory also contains the analogous files for the multiple comparison of any predicted contact list for target 05 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 T05_P11.1.H.complementary_highlighted is partially shown:

    HIGHLIGTHED CONTACT LIST FOR T05_P11.1.H
    Number of Contacts = 160 Matching List_T04_1 = 0/58 Matching List_T05_1 = 1/64 Matching List_T06_1 = 17/65



    .
    . H53 SER - A164 GLY H53 SER - A165 ASP H54 ASP - A63 GLN T06_1 H54 ASP - A104 GLY T06_1 H54 ASP - A105 SER T06_1 H54 ASP - A106 GLY T06_1 H54 ASP - A162 LEU
    .
    .

    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, T05_P04.3.H.highlighted

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T05_P04.3.H
    N_res_Antibody = 23 N_res_Antigen = 22 Match Antibody in List1 = 8/29 Matching Antigen in List1 = 4/25


    AMY07 VHH LIST
    
    H1    GLN    3.255
    H2    VAL   21.583
    H3    GLN    1.620
    H4    LEU    0.989
    H91   TYR   18.892
    H96   PRO   11.293 1
    H97   GLY    7.726 1
    H98   SER   38.664 1
    H99   GLY    8.151
    H100  LYS   95.715 1
    
    .
    . PIG ALPHA-AMYLASE LIST A145 SER 40.092 A147 GLY 15.895 A148 ILE 35.272 A149 GLU 100.244 A150 SER 37.198
    .
    .

    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 interface residues list files and contact list ones are named the same (i.e. T05_P04.3.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 T05_P11.1.H.complementary_highlighted is partially shown:

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T05_P11.1.H
    N_res_Antibody = 42 N_res_Antigen = 57 Matching Antibody in List_T04_1 = 12/27 Matching Antigen in List_T04_1 = 2/37 Matching Antibody in List_T05_1 = 19/29 Matching Antigen in List_T05_1 = 10/25 Matching Antibody in List_T06_1 = 21/29 Matching Antigen in List_T06_1 = 31/37


    AMY07 VHH LIST
    
    H1    GLN  120.374 T06_1
    H2    VAL    0.040 T06_1
    H3    GLN   26.852
    
    .
    . PIG ALPHA-AMYLASE LIST A54 PRO 12.160 T06_1 A58 TRP 22.835 T06_1 A59 TRP 61.415 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 T05_P04.3.H.fitting.summary

    Fitting of A prediction Antigen Subunit onto B CAPRI Antigen Subunit
    Rotation Matrix:
       0.50480  -0.42147  -0.75336
       0.18272  -0.80076   0.57043
      -0.84368  -0.42561  -0.32721
      Translation vector     52.905    60.805    43.822
    Fitting Antibodies, H onto G
    Theta angle = 91.29
    Distance between geometric centres = 27.90008
    

    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 05 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 1-111. In order to be consistent, the distance between geometric centres was calculated taking into account only this antibody fragment.

    Note that in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri_05_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_P11.1.H.J.fitting.complementary.summary:

    Fitting of A prediction Antigen Subunit onto D CAPRI Antigen Subunit
    Rotation Matrix:
      -0.12437  -0.94713  -0.29576
      -0.58356  -0.17126   0.79381
      -0.80249   0.27132  -0.53141
      Translation vector    107.654    82.243    61.356
    Fitting Antibodies, H onto J
    Theta angle = 50.42
    Distance between geometric centres = 11.26566
    

    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.T05_P04.3.H.d looks like that:

    AMY07 VHH Atom    PIG ALPHA-AMYLASE Atom   Distance
    
    --
    H 103  .VAL.N       A 147  .ILE.O           1.37
    H 103  .VAL.O       A 147  .ILE.C           1.63
    H 103  .VAL.CA      A 147  .ILE.O           1.73
    H 103  .VAL.C       A 147  .ILE.O           1.75
    H 103  .VAL.O       A 147  .ILE.O           1.81
    H 103  .VAL.O       A 147  .ILE.N           1.82
    --
    H 103  .VAL.O       A 147  .ILE.CA          2.12
    H 103  .VAL.O       A 146  .GLY.C           2.24
    H 106  .GLY.O       A 162  .VAL.CA          2.25
    H 103  .VAL.C       A 147  .ILE.C           2.32
    H 103  .VAL.O       A 148  .GLU.N           2.35
    
    .
    .

    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.