Get   for     ? 
 Site search     ? 
CAPRI: Critical Assessment of PRediction of Interactions
   Call For Targets
   Meeting Report
   Evaluation Meeting
   Evaluation Meeting
   ROUND 1
   ROUND 2
   ROUND 3
   ROUND 4
   ROUND 5
   ROUND 6
 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 13 evaluation results

Raúl Méndez, Raphaël Leplae and Shoshana J. Wodak.
SCMBB Université Libre de Bruxelles, Cp 263, Brussels, Belgium.
Re-accessed on Friday January 07, 2005.

The evaluation results of the CAPRI Target 13 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 13, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_13_xray.pdb: the crystal structure of the target (Target 13) in PDB format: SAG1-antibody complex.
    Unbound SAG1 molecule is taken from 1KZQ, while the unbound antibody is taken from the complex and randomly oriented.
  • capri_13_xray.AB.contres: list of residue contacts in the target between subunits A and B of antibody (taken as as a Ligand) and subunit F of SAG1.
  • capri_13_xray.AB.intres: list of residue contacts in the target between subunits A and B of antibody (taken as as a Ligand) and subunit F of SAG1.
  • cc.capri_13_xray.AB.d: list of clashes in the interface between antibody and SAG1 subunits.
    Final Summary

    File Target 13 Final Summary. summarizes all the information about the Target 13 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  
    T13_P01.7.HL 0.114 0.877 0.688 0.280 0.611 0.219 864.5 139.7 32.276 46 42.407 5.574 T13_P01.5.HL 0.043 0.961 0.875 0.360 0.718 0.310 839.6 104.6 30.386 46 37.747 6.622 T13_P01.1.HL 0.000 1.000 0.781 0.000 0.862 0.000 821.4 139.2 63.939 69 69.145 12.284 T13_P01.10.HL 0.000 1.000 0.688 0.040 0.595 0.032 822.8 108.3 48.946 37 52.837 11.006 T13_P01.2.HL 0.000 1.000 0.625 0.000 0.645 0.000 888.9 46.3 46.466 42 47.400 12.422

    Again T13_P01.7.HL means participant 01, prediction 7 for the Target 13, Ligand interface HL (antibody as Ligand and SAG1 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 5Å of an atoms of the other.

    Column 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 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 gives the ratio between the residues of the antibody (Ligand) that are part of the interface in the prediction, over the the residues in the equivalent subunits in the target that are part of the interface in the target. The 5th column gives the same information for the residues in the SAG1 (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 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 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 antibody molecule in the predicted complex to that in the target, as for capri_13_xray.pdb. To compute this angle, we first perform a rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) on the SAG1 (predicted SAG1 onto the target SAG1) 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 antibody and the SAG1 molecules 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 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 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.

    Note that for participant P12, predictions 1-3,6-8 the Interface RMSD's couldn't be calculated because coordinates for the corresponding N-terminal fragment on the SAG1 molecules were not provided.

    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 T13_P02.5.HL.highlighted is illustrated in part:

    Number of Contacts = 83 Matching List1 = 53/70

    H28   ASP - A37   THR 1
    H29   ILE - A37   THR
    H30   SER - A36   LYS
    H30   SER - A37   THR 1
    H30   SER - A115  LYS
    H31   ASN - A37   THR
    H31   ASN - A115  LYS
    H32   TYR - A37   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 reference contact list, capri_13_xray.AB.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, T13_P02.5.HL.highlighted

    N_res_Ligand = 34 N_res_Receptor = 27 Match Ligand in List1 = 29/32 Matching Receptor in List1 = 22/25

    H28   ASP 1
    H29   ILE
    H30   SER 1
    H31   ASN 1
    H32   TYR 1
    H49   TYR
    H50   TYR 1
    . L530 THR 1 L531 ASP 1 L532 TYR 1 L533 GLY 1 L550 ILE 1
    . RECEPTOR LIST A14 ASP A36 LYS 1 A37 THR 1 A38 ALA 1 A39 LEU 1

    Each time a residue of the antibody (Ligand) or SAG1 (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_13_xray.AB.intres.

    Note that interface residues list files and contact list ones are named the same (i.e. T13_P02.5.HL.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 T13_P02.5.HL.fitting.summary

    Fitting of A prediction receptor Subunit onto X CAPRI receptor Subunit
    Rotation Matrix:
       0.98293   0.01718  -0.18318
       0.00923   0.98977   0.14234
       0.18376  -0.14160   0.97272
      Translation vector     27.909    -6.173    52.148
    Fitting Ligands, HL onto UV
    Theta angle = 13.42
    Distance between geometric centres = 4.569442

    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 target 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 13 evaluation, the first fit was made using the backbones of the common longest fragment between all SAG1 subunits, residues 2009-2012, 2017-2028, 2030-2035, 2039-2040, 2093-2098, 2104-2111, 2113-2117, 2122-2130; while the second is made using the commong longest fragments of all the dockering subunits, residues 7-9, 19, 39, 41, 68, 70, 73 76, 82, 97, 101 in chain A and residues 501-534, 536-540, 542-614 in chain B. In order to be consistent, the distance between geometric centres was calculated taking into account only this ligand fragment.

    Note that there is a big hinge affecting D2 domain residues from 121 on in the SAG1 molecule upon binding, which is not taken into account for the fittings.

    Note that in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri_13_xray.pdb) were renamed as follows:

    F to X
    for the target SAG1 and
    A to U
    B to V
    for the target antibody.


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

    For example part of file cc.T13_P02.5.HL.d looks like that:

    Ligand Atom         Receptor Atom           Distance
    L 602  .TRP.CE2     A 43   .PRO.CD          1.26
    L 602  .TRP.NE1     A 43   .PRO.CD          1.72
    L 602  .TRP.CG      A 43   .PRO.CG          1.83
    L 600  .SER.O       A 63   .THR.OG1         1.91
    L 602  .TRP.CD2     A 43   .PRO.CG          1.93
    L 602  .TRP.CD2     A 43   .PRO.CD          1.94
    L 602  .TRP.CZ2     A 43   .PRO.CD          1.96
    L 602  .TRP.CD1     A 43   .PRO.CG          2.07
    H 30   .SER.CB      A 37   .THR.OG1         2.15
    L 601  .THR.CG2     A 118  .ASP.OD1         2.16
    L 557  .ASP.OD1     A 52   .GLN.OE1         2.18

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