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CAPRI: Critical Assessment of PRediction of Interactions
 
  
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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 10 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.
e-mail: raul@scmbb.ulb.ac.be
shosh@scmbb.ulb.ac.be

The evaluation results of the CAPRI Target 10 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 10, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_10_xray.pdb: the crystal structure of the target (Target 10) in PDB format: Trimeric form of the TBEV envelope protein.
    The TBEV trimer must be built from the a monomer, subunit A, of pdb id 1SVB.
  • capri_10_xray.A.contres: list of residue contacts in the target between subunit A (taken as as a Ligand) and subunits B and C.
  • capri_10_xray.B.contres: list of residue contacts in the target between subunit B (taken as as a Ligand) and subunits C and A.
  • capri_10_xray.C.contres: list of residue contacts in the target between subunit C (taken as a a Ligand) and subunits A and B
  • capri_10_xray.B.intres: Residues at the interface between A and B, C subunits.
  • capri_10_xray.B.intres: Residues at the interface between B and A, C subunits.
  • capri_10_xray.B.intres: Residues at the interface between C and A, B subunits.
  • cc.capri_10_xray.B.d: list of clashes in the interface between A and B, C subunits.
  • cc.capri_10_xray.B.d: list of clashes in the interface between B and A, C subunits.
  • cc.capri_10_xray.B.d: list of clashes in the interface between C and A, B subunits.
    Final Summary

    File Target 10 Final Summary. summarizes all the information about the Target 10 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  
    
    T10_P01.1.C 0.000 1.000 0.007 0.031 0.024 0.091 1218.0 45.0 46.803 114 51.090 29.485 T10_P01.10.C 0.000 1.000 0.000 0.008 0.000 0.111 355.0 72.4 50.732 57 56.244 31.138 T10_P01.2.B 0.000 1.000 0.022 0.031 0.088 0.114 1236.6 38.9 50.813 291 55.199 31.053 T10_P01.3.C 0.000 1.000 0.022 0.008 0.094 0.031 675.4 61.7 49.860 31 54.979 30.197 T10_P01.4.C 0.000 1.000 0.000 0.038 0.000 0.357 458.9 41.6 51.780 83 55.887 30.832
    .
    .

    Again T10_P01.1.C means participant 01, prediction 1 for the Target 10, Ligand interface C. This time "Ligand" and "Receptor" names don't make sense, since all the subunits are equal in terms of sequence identity. But these tags have been manteined as to indicate that "interface C is the interface made between C and A, B.

    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 subunit considered as a 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 subunits considered as being "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 Ligand molecule in the predicted complex to that in the target, as for capri_10_xray.pdb. To compute this angle, we first perform series of rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) on each possible couple of subunits between the prediction and target applying the transformation to the whole trimer in the prediction. The fit that leaves the non-fitted subunits closer to their equivalents in the target is taken as a reference. The fitted subunits are considered as a "Receptors" (one for the prediction and one for the Target) while the remaining two others are considered as "Ligands", although here the terms are really ambiguous, since the label in the summary table can be interpreted as a "Receptor", instead of as usual, as "Ligand". One could also see this process as fitting "Ligands" (single chains) leaving Receptor molecules free. To better understand what's going on see FittingSummary section for a particular file.

    After this first fit, a second fit is performed (starting after the application of the trasnformation of the first fit to the whole predicted trimer) 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 Ligand and the Receptor 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.


    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 T10_P17.10.B.highlighted is illustrated in part:

    HIGHLIGTHED CONTACT LIST FOR T10_P17.10.B
    Number of Contacts = 150 Matching List1 = 80/272 Matching List2 = 79/265 Matching List3 = 79/267



    B24   VAL - C168  SER
    B54   ALA - A216  HIS
    B55   LYS - A216  HIS
    B56   THR - A216  HIS
    B56   THR - A218  ASP 1 2 3
    
    .
    .

    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 capri_10_xray.A.contres reference contact list, "2" to capri_10_xray.B.contres and "3" to capri_10_xray.C.contres reference contact list.


    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, T10_P17.10.B.highlighted

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T10_P17.10.B
    N_res_Ligand = 64 N_res_Receptor = 66 Match Ligand in List1 = 59/135 Matching Receptor in List1 = 58/131 Match Ligand in List2 = 58/134 Matching Receptor in List2 = 59/133 Match Ligand in List3 = 59/130 Matching Receptor in List3 = 59/135


     LIGAND LIST
    
    B24   VAL 1 2 3
    B54   ALA 1 2 3
    B55   LYS 1 2 3
    B56   THR 1 2 3
    
    .
    . RECEPTOR LIST A24 VAL 1 2 3 C54 ALA 1 2 3 C55 LYS 1 2 3 C56 THR 1 2 3 C57 ARG 1 2 3
    .
    .

    Each time a residue of the considered as Ligand or 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 capri_10_xray.A.intres reference list, "2" for capri_10_xray.B.intres and "3" for capri_10_xray.C.intres lists.

    Note that interface residues list files and contact list ones are named the same (i.e. T10_P17.10.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 T10_P17.10.B.fitting.summary

    Fitting of B prediction receptor Subunit onto Z CAPRI receptor Subunit
    Rotation Matrix:
      -0.84302  -0.39703  -0.36289
      -0.26372   0.89309  -0.36447
       0.46880  -0.21156  -0.85760
      Translation vector      4.309    18.488    72.258
    Fitting Ligands, AC onto XY
    Theta angle = 3.63
    Distance between geometric centres = 1.482805
    

    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 target ligand after this first fit (considering just the fragment that is fitted in the second fit) and the Theta angle of the second fit.

    Note that again here there is an ambiguity between what we call "Receptor" and "Ligand". According to Target 10 Final Summary ".B" would stand for the name of the "Ligand" molecule, but here in this context in fact "B" is the first subunit of the prediction that was fitted onto its equivalent on the target, so it's acting as our classical Receptor. The same for subunits A and C, they are used in the second fit, after C is well placed, so acting as our classical "Ligand".

    For this Target 10 evaluation, the first fit was made using the backbones of the common longest fragment between all subunits, residues 40-143, 192-203 and 210-291.In order to be consistent, the distance between geometric centres was calculated taking into account only this ligand fragment.

    These fragments also skip the the C- terminal domain (domain III) of TBEV that undergoes on a hinge upon the formation of the trimer from the dimer at 1SVB structure.

    Note that in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri_10_xray.pdb) were renamed as follows:

    A to X
    B to Y
    C to Z.


    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.T10_P17.10.B.d looks like that:

    Ligand Atom         Receptor Atom           Distance
    
    --
    B 222  .ASP.OD2     C 229  .HIS.NE2         2.64
    B 229  .HIS.NE2     A 222  .ASP.OD2         2.64
    B 244  .PHE.O       C 86   .HIS.NE2         2.64
    
    .
    .

    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 (no contacts also). Empty files means, no close contacts found.