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áMSDá 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 15 evaluation results

Ra˙l MÚndez, RaphaŰl Leplae and Shoshana J. Wodak.
SCMBB UniversitÚ Libre de Bruxelles, Cp 263, Brussels, Belgium.
Friday August 13, 2004.
e-mail: raul@scmbb.ulb.ac.be
shosh@scmbb.ulb.ac.be

The evaluation results of the CAPRI Target 15 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 15, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_15_xray.pdb: the crystal structure of the target (Target 15) in PDB format: Colicin D catalytic domain complexed with Colicin D immunity protein. Coordinates for both, Colicin D catalytic domain and Colicin D immunity protein, are taken from the complex and shaved to their C-beta.
  • capri_15_xray.B.contres: list of residue contacts in the target between subunit B of Colicin D immunity protein (considered as a Ligand) and subunit A of Colicin D catalytic domain (considered as a Receptor).
  • capri_15_xray.B.intres: list of residues at the interface in the target between subunit B of Colicin D immunity protein (considered as a Ligand) and subunit A of Colicin D catalytic domain (considered as a Receptor).
  • cc.capri_15_xray.B.d: list of clashes in the interface between Colicin D immunity protein and Colicin D catalytic domain subunits.
    Final Summary

    File Target 15 Final Summary. (or use TEXT ONLY version) summarizes all the information about the Target 15 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  
    
    T15_P44.1.B 0.000 1.000 0.000 0.077 0.000 0.077 945.3 99.7 36.526 120 39.957 16.402 T15_P44.10.B 0.000 1.000 0.154 0.000 0.200 0.000 635.2 126.7 43.306 19 47.423 19.949 T15_P44.2.B 0.000 1.000 0.000 0.000 0.000 0.000 1151.3 153.9 39.265 121 44.301 17.377 T15_P44.3.B 0.000 1.000 0.346 0.000 0.375 0.000 1034.6 102.1 38.733 136 41.511 14.600 T15_P44.4.B 0.000 1.000 0.462 0.000 0.429 0.000 923.8 130.9 39.232 37 42.029 15.298 T15_P44.5.B 0.000 1.000 0.192 0.000 0.217 0.000 829.7 174.7 41.058 63 46.603 18.282 T15_P44.6.B 0.000 1.000 0.500 0.038 0.500 0.033 869.1 120.4 38.288 22 41.512 15.535 T15_P44.7.B 0.000 1.000 0.462 0.000 0.522 0.000 1050.9 125.3 38.756 145 42.890 15.251 T15_P44.8.B 0.000 1.000 0.577 0.000 0.556 0.000 948.2 154.1 38.822 90 42.609 13.843
    .
    .

    Again T15_P44.1.B means participant 44, prediction 1 for Target 15, Ligand interface B (Colicin D immunity protein as Ligand and Colicin D catalytic domain 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 Colicin D immunity protein (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 Colicin D catalytic domain (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 Colicin D immunity protein molecule in the predicted complex to that in the target, capri_15_xray.pdb. To compute this angle, we first perform a rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) on the Colicin D catalytic domain (predicted Colicin D catalytic domain onto the target Colicin D catalytic domain) 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 Colicin D immunity protein and the Colicin D catalytic domain 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 T15_P75.3.B.highlighted is illustrated in part:

    HIGHLIGTHED CONTACT LIST FOR T15_P75.3.B
    Number of Contacts = 54 Matching List1 = 50/56



    B24   SER - A610  LYS 1
    B25   GLU - A610  LYS 1
    B25   GLU - A622  LYS 1
    B28   CYS - A610  LYS 1
    B28   CYS - A611  HIS 1
    B31   ARG - A614  ASP 1
    B31   ARG - A680  LYS 1
    B31   ARG - A681  ILE 1
    B31   ARG - A682  ASN 1
    B32   ARG - A610  LYS 1
    B32   ARG - A611  HIS 1
    B32   ARG - A613  GLY 1
    B32   ARG - A614  ASP 1
    B35   TYR - A680  LYS 1
    B35   TYR - A681  ILE 1
    B35   TYR - A682  ASN 1
    B35   TYR - A683  PRO 1
    B36   GLY - A682  ASN 1
    B45   LEU - A682  ASN 1
    B45   LEU - A684  ASP 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_15_xray.B.contres.


    INTERFACE_RESIDUES_HIGHLIGHTED

    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, T15_P75.3.B.highlighted

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T15_P75.3.B
    N_res_Ligand = 25 N_res_Receptor = 26 Match Ligand in List1 = 23/26 Matching Receptor in List1 = 25/26


     
     LIGAND LIST
    
    B24   SER 1
    B25   GLU 1
    B28   CYS 1
    B29   VAL 1
    B31   ARG 1
    
    .
    . RECEPTOR LIST A603 LYS 1 A604 GLN A607 LYS 1 A608 LYS 1 A610 LYS 1 A611 HIS 1 A613 GLY 1
    .
    .

    Each time a residue of the Colicin D immunity protein (Ligand) or Colicin D catalytic domain (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_15_xray.B.intres.

    Note that interface residues list files and contact list ones are named the same (i.e. T15_P75.3.B.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 T15_P75.3.B.fitting.summary

    Fitting of A 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      0.000     0.000     0.000
    Fitting Ligands, B onto U
    Theta angle = 0.96
    Distance between geometric centres = 0.6075816
    

    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 Colicin D immunity protein and target Colicin D immunity protein 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 15 evaluation, the first fit was made using the backbones of the common longest fragment between all Colicin D catalytic domain subunits, residues 591-697 while the second is made using the common longest fragments of all the Colicin D immunity protein subunits, residues 1-87. In order to be consistent, the distance between geometric centres was calculated taking into account only this ligand 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_15_xray.pdb) were renamed as follows:

    A to X
    for the target Colicin D catalytic domain and
    B to U
    for the target Colicin D immunity protein.


    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.T15_P75.3.B.d looks like that:

    Ligand Atom         Receptor Atom           Distance
    
    --
    B 59   .GLU.OE2     A 607  .LYS.NZ          2.64
    B 46   .ASN.OD1     A 686  .ASP.N           2.65
    B 56   .GLU.OE2     A 677  .SER.OG          2.67
    B 56   .GLU.OE1     A 611  .HIS.NE2         2.81
    B 61   .ASP.OD2     A 607  .LYS.NZ          2.81
    

    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 (no contacts also) and 2-3┼. Empty files mean, no close contacts found.