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

Hosted By EMBL/EBI-MSD Group

CAPRI Target 19 evaluation results

Ra˙l MÚndez, RaphaŰl Leplae and Shoshana J. Wodak.
SCMBB UniversitÚ Libre de Bruxelles, Cp 263, Brussels, Belgium.
Friday August 13, 2004.

The evaluation results of the CAPRI Target 19 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.


Directory Information contains the information about Target 19, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_19_xray.pdb: the crystal structure of the target (Target 19) in PDB format: Fab antibody complexed with ovine prion. Coordinates for the fab are taken from the complex, and for the ovine prion are taken from 1DWY pdb entry (NMR ensemble) + homology modelling.
  • capri_19_xray.A.contres: list of residue contacts in the target between subunit B of ovine prion (considered as a Ligand) and subunit A of Fab antibody (considered as a Receptor).
  • capri_19_xray.A.intres: list of residues at the interface in the target between subunit B of ovine prion (considered as a Ligand) and subunit A of Fab antibody (considered as a Receptor).
  • cc.capri_19_xray.A.d: list of clashes in the interface between ovine prion and Fab antibody subunits.
    Final Summary

    File Target 19 Final Summary. (or use TEXT ONLY version) summarizes all the information about the Target 19 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)		THETA ANGLE	DISTANCE	    Nclash		  L_rmsd	   I_rmsd
    								   Ligand    	Receptor  	   Ligand    	Receptor  
    T19_P12.8.A 0.568 0.343 0.800 0.828 0.769 0.828 959.4 13.4 3.851 6 4.672 1.258 T19_P12.2.A 0.407 0.598 0.800 0.897 0.625 0.839 1164.0 24.2 2.908 6 5.055 2.582 T19_P12.10.A 0.272 0.639 0.720 0.793 0.643 0.821 1008.9 26.0 6.146 6 7.629 2.876 T19_P12.5.A 0.062 0.941 0.840 0.448 0.700 0.433 1023.2 141.9 18.076 15 25.720 9.330 T19_P12.6.A 0.012 0.986 0.720 0.448 0.720 0.433 850.7 140.2 19.986 9 27.386 9.472 T19_P12.9.A 0.012 0.988 0.160 0.655 0.138 0.594 1076.6 101.2 9.169 7 19.485 11.344

    Again T19_P12.8.A means participant 12, prediction 8 for Target 19, Ligand interface B (ovine prion as Ligand and Fab antibody as 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 5┼ 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 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 terms of contacts: 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 gives the ratio between the residues of the ovine prion (Ligand) that are part of the interface in the prediction, over the the residues in the equivalent subunit in the target that are part of the interface in the target. The 5th column gives the same information for the residues in the Fab antibody (Receptor). All the interface residues lists are generated using the BRUGEL package, as the residues having ASA(unbound)- ASA(in the complex) > 0. Note that this time we don't use the Connolly algorithm. We compute the interface area for each pair of residues in contact using polygons instead of spherical cups, being this way less accurate but less demaning in terms of quality of the structure.

    Columns 6 and 7 list 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 ┼2), calculated as the sum of interface areas per each pair of residues in contact implemented also in the BRUGEL package.

    Column 9 lists the rotation angle (Theta angle) necessary to fit the ovine prion molecule in the predicted complex to that in the target, capri_19_xray.pdb. To compute this angle, we first perform a rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) on the Fab antibody (predicted Fab antibody onto the target Fab antibody) and apply the translation-rotation transformation to the whole predicted complex.

    After this first fit, a second fit is performed (starting from the previous situation)so as to superimpose the predicted "Ligand" molecules onto its closest counterpart in the target structure. 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 Ligand 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 Ligands in the prediction relative to the position in the target.

    Column 11 lists the number of clashes Nclash between the ovine prion and the Fab antibody molecules for each predicted complex. Clashes are computed between heavy atoms within 3 ┼ . 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 ┼.

    Columns 12 and 13 list the RMSD's (Root Mean Square Deviation) values in ┼ . Column 11 list the RMSD values calculated between the Ligand's backbones once the corresponding Receptors are superimposed (Ligand RMSD or L_rmsd). Column 12 contains the rsmd's when sumperimposing the backbones of the residues at the interface 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 ┼ 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 T19_P94.4.A.highlighted is illustrated in part:

    Number of Contacts = 81 Matching List1 = 60/81

    A124  GLY - H54   THR 1
    A125  LEU - H53   PHE 1
    A125  LEU - H54   THR 1
    A149  TYR - L53   ARG 1
    A153  ASN - L53   ARG 1
    A155  TYR - L30A  ASP 1
    A155  TYR - L30B  GLY 1
    A155  TYR - L30C  LYS 1
    A156  ARG - L30C  LYS 1
    A156  ARG - L49   TYR 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 reference contact list, capri_19_xray.A.contres.


    Directory InterfaceResidues contains one file per predicted interface, with information on the residues forming the different interfaces in the prediction and how well they match those in the target interfaces.

    The information contained in each file is illustrated by an example, T19_P94.4.A.highlighted

    N_res_Ligand = 28 N_res_Receptor = 29 Match Ligand in List1 = 24/25 Matching Receptor in List1 = 26/29

    A124  GLY 1
    A125  LEU 1
    A128  TYR
    A149  TYR 1
    A153  ASN 1
    A155  TYR 1
    . RECEPTOR LIST H28 THR 1 L29B ASP 1 L30C LYS 1 L30B GLY 1 L30A ASP 1 L30 SER H31 ASN 1

    Each time a residue of the ovine prion (Ligand) or Fab antibody (Receptor) molecules in the predicted interface interface matches one of the interface residues in the target list, it is highlighted with the number of the corresponding target reference list. Analogously "1" stands for the only interface residue reference list capri_19_xray.A.intres.

    Note that interface residues list files and contact list ones are named the same (i.e. T19_P94.4.A.highlighted) but they are in different directories and their contents are completely different.


    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 T19_P94.4.A.fitting.summary

    Fitting of HL prediction receptor Subunit onto XY CAPRI receptor Subunit
    Rotation Matrix:
       0.29088   0.95100   0.10480
      -0.95627   0.29249   0.00000
      -0.03065  -0.10022   0.99449
      Translation vector   -128.854  -421.276   -46.423
    Fitting Ligands, A onto U
    Theta angle = 18.67
    Distance between geometric centres = 2.860568

    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 ovine prion and target ovine prion 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 19 evaluation, the first fit was made using the backbones of the common longest fragment between all Fab antibody subunits, residues H2-5, H7-10, H12-24, H26-31, H33-35, H37-35, H37-52, H53-75, H77-81, L3-28, L31-104 while the second is made using the common longest fragments of all the ovine prion subunits, residues A132-143, A147-157, A159-169, A174-175, A177-188, A190-196, A199-207, A210-211. In order to be consistent, the distance between geometric centres was calculated taking into account only this ligand fragment.

    Note that the discontinuity on the intervals for the ovine prion skipps the small conformational changes between unbound 1DWY and target prions, residues A144-145, A170-173 and A197-198.

    Note that in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri_19_xray.pdb) were renamed as follows:

    H to X
    L to Y
    for target Fab antibody and
    A to U
    for target ovine prion.


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

    For example part of file cc.T19_P94.4.A.d looks like that:

    Ligand Atom         Receptor Atom           Distance
    A 185  .LYS.CE      H 53   .PHE.CG          0.78
    A 185  .LYS.CE      H 53   .PHE.CD1         0.89
    A 185  .LYS.NZ      H 53   .PHE.CD1         1.07
    A 188  .THR.CG2     H 31   .ASN.O           1.30
    A 196  .GLU.OE1     L 50   .LEU.CG          1.55
    A 196  .GLU.OE2     L 49   .TYR.CD1         1.65
    A 185  .LYS.CE      H 53   .PHE.CB          1.66
    . -- A 185 .LYS.CE H 53 .PHE.CD2 2.11 A 197 .ASN.OD1 L 49 .TYR.CG 2.15 A 185 .LYS.CD H 53 .PHE.CG 2.21 A 185 .LYS.CE H 53 .PHE.CE1 2.21 A 193 .THR.O L 96 .GLN.NE2 2.23

    As in the evaluation of target 01, the list of clashes is segregated into clashes between 0-1, 1-2 and 2-3 ┼. Empty files mean, no close contacts found.