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CAPRI: Critical Assessment of PRediction of Interactions
 
  
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 MSD  CAPRI: Critical Assessment of PRediction of Interactions

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

Hosted By EMBL/EBI-MSD Group

CAPRI Target 08 evaluation results

Raúl Méndez, Raphaël Leplae and Shoshana J. Wodak.
SCMBB Université Libre de Bruxelles, Cp 263, Brussels, Belgium.
Monday May 5, 2003.
e-mail: raul@ucmb.ulb.ac.be
shosh@ucmb.ulb.ac.be

The evaluation results of the CAPRI target 08 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 08, that was used in the evaluation and scoring. It contains the following files (file names are given in bold): The Directory Information is password locked

  • capri_08_xray.pdb: the crystal structure of the target (target 08) in PDB format: Laminin EGF-like complex Nidogen-G3 domain.
  • capri_08_xray.B.contres: list of residue contacts in the target between Nidogen subunit and Laminin EGF-like modules.
  • capri_08_xray.B.intres: Nidogen - G3 Laminin EGF interface residues.
  • cc.capri_08_xray.B.d: list of clashes in the target interface.
    Final Summary

    File target 08 Final Summary. summarizes all the information about the target 08 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) IA(A2) THETAANGLE   DIST  Nclash L_rmsd   I_rmsd
                                 Ligand  Receptor  Laminin  Receptor  
    
    T08_P01.2.A 0.530 0.286 0.769 0.967 0.231 0.121 1867.4 24.1 4.015 3 4.628 0.663 T08_P01.10.A 0.045 0.940 0.731 0.467 0.345 0.500 1677.5 40.7 20.311 0 21.067 3.407 T08_P01.7.A 0.015 0.977 0.269 0.500 0.632 0.348 1307.7 53.0 16.120 2 18.059 2.808 T08_P01.1.A 0.000 1.000 0.308 0.133 0.619 0.789 1257.6 59.6 45.086 2 45.959 10.446 T08_P01.3.A 0.000 1.000 0.269 0.067 0.611 0.917 1368.9 83.9 38.294 3 39.387 7.612
    .
    .

    Again T08_P01.2.A means participant 01, prediction 2 for the target 08, Ligand interface A. For simplicity we call the smallest molecule (Laminin), the Ligand and the biggest (Nidogen) the Receptor.

    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 non native predicted contacts (over prediction). This fraction is computed as the number of contacts in the prediction that doesn'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 Laminin that are part of the interface in the prediction, over the Laminin residues that are part of the interface in the target. The 5th column gives the same information for the Nidogen 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 interface Area (in Å2), calculated as IA = ASA(ligand) + ASA(receptor) - ASA(complex). For ASA (Accessible Surface Area) calculations we used Conolly the (Conolly, M.L. 1985, J. Mol. Biology., 107, 1118 - 1124) and Richmon (Richmon, T. J. 1984, J. Mol. Biol., 178, 63-89) algorithm, implemented also in the BRUGEL package.

    Column 9 lists the rotation angle (Theta angle) necessary to fit the Laminin molecule in the predicted complex to that in the target, as per capri_08_xray.pdb. To compute this angle, we first perform a rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) of the Nidogen subunit in the predicted complex, to the Nidogen subunit in the target.

    After this first fit, a second fit is performed so as to superimpose the predicted Laminin molecules onto its closest counterpart in the target structure (capri_08_xray.pdb closest). The rotation angle corresponding to this second fitting is the listed theta angle.

    Column 10 lists the distance (in Angstroms) between geometric centers of predicted and target Laminin molecules before the second fit. The distance between the geometric centers together with the Theta angle gives an idea of the global position of the Laminin in the prediction relative to the position in the target.

    Column 11 lists the number of clashes Nclash between the Laminin and the Nidogens 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 12 and 13 list the RMSD's (Root Mean Square Deviation) values in Å . Column 11 list the RMSD values calculated between the Laminin's backbones once the Nidogens are superimposed (Ligand RMSD or L_rmsd). Column 12 contains the rsmd's when sumperimposing the backbones of the residues at the interface (Laminin + Nidogen) on the prediction upon the counterpart in the target. Residues at the interface (Interface RMSD or I_rmsd) 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, but in the case of the interface RMSD's, restricted to the residues at the interface, according to this new definition.


    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 T08_P01.2.A.highlighted is illustrated in part:

    HIGHLIGTHED CONTACT LIST FOR T08_P01.2.A
    Number of Contacts = 49 Matching List1 = 35/66



    A32   HIS - B1160 HIS 1
    A32   HIS - B1161 LYS 1
    A33   CYS - B1161 LYS 1
    A38   ALA - B921  THR 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.


    INTERFACE_RESIDUES_HIGHLIGHTED

    Directory InterfaceResidues contains one file per predicted interface, with information on the residues forming the Nidogen - Laminin 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, T08_P01.2.A.highlighted

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T08_P01.2.A
    N_res_Ligand = 26 N_res_Receptor = 33 Match Ligand in List1 = 20/26 Matching Receptor in List1 = 29/30


    Ligand LIST
    
    A32   HIS   71.418 1
    A33   CYS   20.789 1
    A37   THR    2.334 1
    A38   ALA   30.293 1
    A39   GLY   35.505 1
    
    .
    . Target LIST B921 THR 67.194 1 B922 GLY 8.148 1 B923 LYS 2.333 1 B944 HIS 39.075 1 B946 PRO 92.126 1
    .
    .

    Each time a residue of the Laminin or Nidogen 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. T08_P01.2.A.highlighted) but they are in different directories and their contents are completely different.


    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 T08_P01.2.A.fitting.summary

    Fitting of B prediction receptor Subunit onto X CAPRI receptor Subunit
    Rotation Matrix:
       1.00000   0.00000   0.00000
       0.00000   1.00000   0.00000
       0.00000   0.00000   1.00000
      Translation vector    -15.000   -15.000   -15.000
    Fitting Ligands, A onto Y
    Theta angle = 24.12
    Distance between geometric centres = 4.014677
    

    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 ligand and Capri ligand 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 08 evaluation, the first fit was made using the backbones of the common longest fragment Nidogen subunit, residues 913-1175 while the second fit was made considering the common longest ligand fragments to all the participants, e.g. residues 793-799, 806-815 and 817-847. In order to be consistent, the distance between geometric centres was calculated taking into account only this ligand fragment.

    Note that most of the times (if the participants didn't change signficatively the secondary structure) for the first fit the transformation matrix is the identity matrix, because the provided unbound coordinates for the Nidogen are in fact comming from the bound complexes, and ramdomly oriented.

    Note that in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri_08_xray.pdb) were renamed as follows:

    A to X
    for the Nidogen subunit
    B to Y
    for the Laminin ligand subunit.


    FITTED PDB

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


    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.T08_P01.2.A.d looks like that:

    Ligand Atom         Receptor Atom           Distance
    
    --
    A 47   .ASP.OD2     B 1166 .TYR.OH          2.82
    A 89   .LYS.NZ      B 992  .SER.OG          2.88
    A 73   .ASP.OD2     B 1055 .ARG.NH2         2.98
    
    .
    .

    As in the evaluation of target 01, the list of clashes is segregated into clashes between 0-1, 1-2 (no contacts in this case and 2-3Å. Empty files means, no close contacts found.