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

Round 6 CAPRI community wide experiment on the comparative evaluation of protein-protein docking for structure prediction

Hosted By EMBL/EBI-MSD Group

CAPRI Target 20 evaluation results

Raúl Méndez, Marc F. Lensink and Shoshana J. Wodak.
SCMBB Université Libre de Bruxelles, Cp 263, Brussels, Belgium.
Thursday June 02, 2005.
raul{at}scmbb.ulb.ac.be
lensink{at}scmbb.ulb.ac.be
shoshana{at}sickkids.ca

The evaluation results of the CAPRI Target 20 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 20, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_20_xray.pdb: the crystal structure of the target (Target 20) in PDB format: protein Methyltransferase HEMK complexed with Release Factor 1 (RF1). Coordinates for HEMK are taken from pdb entry 1T43, while RF1 SHOULD BE HOMOLOGY MODELLED from pdb entry 1GQE, the structure for the RF2 homolog.
  • capri_20_xray.A.contres: list of residue contacts in the target between subunit A of HEMK (considered as a Ligand) and subunit B of RF1 (considered as a Receptor).
  • capri_20_xray.A.intres: list of residues at the interface in the target between subunit A of HEMK (considered as a Ligand) and subunit B of RF1 (considered as a Receptor).
  • cc.capri_20_xray.A.d: list of clashes in the interface between HEMK and RF1 subunits.
    Final Summary

    File Target 20 Final Summary (or use TEXT ONLY version) summarizes all the information about the Target 20 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_rmsdbb	I_rmsdsc
							Ligand		Receptor   	Ligand		Receptor   

    
T20_P02.1.B  		  0.167		  0.672		  0.441		  0.512		  0.333		  0.250		 2057.2		  113.7		 23.512		   3		 39.662		 10.194		 10.811
T20_P02.10.B 		  0.193		  0.694		  0.475		  0.463		  0.300		  0.321		 2024.1		  168.3		 26.142		   8		 45.451		 15.868		 16.942
T20_P02.2.B  		  0.175		  0.692		  0.441		  0.537		  0.366		  0.154		 2133.3		  130.3		 22.470		   4		 41.261		 12.079		 12.826
T20_P02.3.B  		  0.184		  0.638		  0.458		  0.366		  0.250		  0.250		 1689.3		  157.1		 24.604		   6		 44.186		 14.953		 15.966
T20_P02.4.B  		  0.263		  0.663		  0.678		  0.585		  0.149		  0.143		 2498.6		  126.5		 20.085		   8		 39.734		  9.839		 10.782

    .

    .

    Again T20_P02.1.B means participant 50, prediction 1 for the Target 20, Ligand interface B (HEMK as Ligand and RF1 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.

  • 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 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 HEMK (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 RF1 (Receptor). All the interface residues lists are generated using the program Naccess, as the residues having ASA(unbound)- ASA(in the complex) > 0. Note that Naccess uses Lee and Richards algorithm (J.Mol.Biol 1977;55:379-400) to compute accessible surface area

  • 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 Å2), calculated as by Naccess program.

  • Column 9 lists the rotation angle (Theta angle) necessary to fit the HEMK molecule in the predicted complex to that in the target, as for capri_20_xray.pdb. To compute this angle, we first perform a rigid-body fit on the RF1 (predicted RF1 onto the target RF1) and apply the translation-rotation transformation to the whole predicted complex. Molecular fits were computed using the McLachlan algorithm (Acta Cryst A 1982; A3:871-873) as implemented in the program ProFit.

    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. Theta angles are then computed using the program DynDom (Proteins 1998;30:144-154)

  • 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 HEMK and the RF1 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, 13 and 14 list the RMSD's (Root Mean Square Deviation) values in Å . Column 12 list the RMSD values calculated between the Ligand's backbones once the corresponding Receptors are superimposed (Ligand RMSD or L_rmsd). Column 13 contains the rsmd's when superimposing the backbones of the residues at the interface on the prediction upon the counterpart in the target. Residues at the interface (Interface backbone RMSD or I_rmsdbb) 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. Column 14 contains the rmsd's when superimposing the SIDE CHAINS of the resdiues at the interface (Interface side chain RMSD or I_rmsdsc), defined according to the 10 Å criterion. For Ligand 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 the 10 Å definition. Again here, RMSD and fits are performed using the program ProFit.

    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 T20_P50.4.A.highlighted is illustrated in part:

    HIGHLIGTHED CONTACT LIST FOR T20_P50.4.A
    Number of Contacts = 84 Matching List1 = 39/114 


    A8    ARG - B159  TYR
A11   ILE - B153  GLU
A18   GLU - B239  THR 1
A18   GLU - B240  THR 1
A19   SER - B240  THR 1
A19   SER - B241  ASP
A21   ARG - B151  ALA
A21   ARG - B152  SER
A21   ARG - B153  GLU 1
A21   ARG - B159  TYR
A21   ARG - B258  GLN
A22   ARG - B241  ASP 1
A22   ARG - B242  SER
A22   ARG - B243  ALA
A22   ARG - B258  GLN 1
A22   ARG - B260  GLU 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_20_xray.A.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, T20_P50.4.A.highlighted

    HIGHLIGHTED INTERFACE RESIDUE LIST FOR T20_P50.4.A
    N_res_Ligand = 54 N_res_Receptor = 39 Match Ligand in List1 = 45/59 Matching Receptor in List1 = 33/41 

     
 LIGAND LIST

A4    GLN   13.380
A8    ARG   39.760
A11   ILE   21.460 1
A17   SER    2.080
A18   GLU   39.960 1
A19   SER   46.290 1
A20   PRO    0.990
A21   ARG  104.530 1
A22   ARG  125.360 1

    .

    .
 RECEPTOR LIST

B132  PHE    3.080 1
B140  GLU   19.990 1
B146  VAL   25.050 1
B147  GLU   27.540 1
B148  ILE   63.660 1
B151  ALA   17.690 1
B153  GLU   67.600 1

    .

    .

    Each time a residue of the HEMK (Ligand) or RF1 (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. For each residue its buried area it is indicated in Å2. Analogously "1" stands for the only interface residue reference list capri_20_xray.A.intres.

    Note that interface residues list files and contact list ones are named the same (i.e. T20_P50.4.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 T20_P50.4.A.fitting.summary

    Fitting of B prediction receptor Subunit onto Y CAPRI receptor Subunit
Rotation matrix
     0.1132   0.7567  -0.6439
     0.2708  -0.6470  -0.7128
    -0.9560  -0.0937  -0.2781
Translation vector          78.2376 -109.9655  84.9694

Fitting Ligands, A onto Z
Theta angle =  16.665
Distance between geometric centres =   5.989

    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 HEMK and target HEMK 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 in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri_20_xray.pdb) were renamed as follows:

    A to Z
    for the target HEMK molecules and
    B to Y
    for the target RF1 molecues

    For this Target 20 evaluation, the first fit was made using the backbones of the common longest fragment between all RF1 subunits, residues, not affected by any conformartional change (as defined by our pairwise structural alignment server wwwsup). These residues were, for chain Y in the target: 107, 113, 117-118, l23-124, 128, 133, 135, 137, 139-140, 147-148, 152-152, 154, 160, 165-169, 172-173, 175, 178, 180, 182-183, 186, 197-199, 205, 207-208, 254, 257, 262-267, 270, 276.

    The second fit is made using the common longest fragments of all the HEMK subunits not affected by any conformational change (defined as for the receptor RF1 molecules). These residues are for chain Z in the target: 74-76, 79-103, 111-172, 177-225, 232-246, 248-254, 256-265, 269-274. In order to be consistent, the distance between geometric centres was calculated taking into account only these ligand fragments.

    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.T20_P50.4.A.d looks like that: 

    Ligand Atom          Receptor Atom         Distance

--
A 207   .LEU.O       B 235   .GLN.OE1          2.35
A 186   .TYR.N       B 235   .GLN.OE1          2.35
A 22    .ARG.NE      B 241   .ASP.OD2          2.80
A 193   .HIS.O       B 236   .HIS.NE2          2.84
A 76    .GLU.OE1     B 261   .ARG.NH1          2.86
A 185   .PRO.CA      B 235   .GLN.OE1          2.87
A 21    .ARG.NH1     B 153   .GLU.OE1          2.87
A 36    .ARG.NH2     B 258   .GLN.O            2.88
A 76    .GLU.OE1     B 261   .ARG.NE           2.89
A 207   .LEU.CD2     B 235   .GLN.O            2.96
A 207   .LEU.CG      B 235   .GLN.O            2.98
A 36    .ARG.NH2     B 260   .GLU.O            2.99

    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 2-3Å. Empty files mean, no close contacts found.