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

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CAPRI Target 14 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 14 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 14, that was used in the evaluation and scoring. It contains the following files (file names are given in bold):

  • capri_14_xray.pdb: the crystal structure of the target (Target 14) in PDB format: protein Ser/Thr phosphatase-1 complexed with Myosin Phosphatase targeted subunit 1 (MYPT1). Coordinates for Ser/Thr phospha tase are taken from 1FJM + homology modelling. MYPT1 is taken from the complex
  • capri_14_xray.B.contres: list of residue contacts in the target between subunit B of MYPT1 (considered as a Ligand) and subunit A of protein Ser/Thr phosphatase-1 (considered as a Receptor).
  • capri_14_xray.B.intres: list of residues at the interface in the target between subunit B of MYPT1 (considered as a Ligand) and subunit A of protein Ser/Thr phosphatase-1 (considered as a Receptor).
  • cc.capri_14_xray.B.d: list of clashes in the interface between MYPT1 and protein Ser/Thr phosphatase-1 subunits.
    Final Summary

    File Target 14 Final Summary. (or use TEXT ONLY version) summarizes all the information about the Target 14 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  
    T14_P12.8.B 0.529 0.245 0.553 0.765 0.894 0.897 1778.0 6.2 2.919 12 3.827 0.949 T14_P12.3.B 0.019 0.974 0.579 0.235 0.830 0.276 1754.7 176.7 56.323 16 65.496 15.207 T14_P12.7.B 0.006 0.990 0.553 0.118 0.824 0.157 1607.0 154.1 55.640 8 68.992 14.493 T14_P12.1.B 0.000 1.000 0.500 0.191 0.905 0.271 1476.5 88.0 38.656 10 47.194 10.811 T14_P12.10.B 0.000 1.000 0.158 0.059 0.324 0.114 1111.4 107.4 59.298 11 69.149 19.410

    Again T14_P12.8.B means participant 12, prediction 8 for Target 14, Ligand interface B (MYPT1 as Ligand and protein Ser/Thr phosphatase-1 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. Note that there is a C-terminal fragment in the target Ser/Thr phosphatase-1 (residues 299-309) which is not provided in the unbound form, making high number of contacts with the MYPT1. Therefore, the number of native contacts it is higher than the predicted one, this results in a slightly understimation of the fraction of predicted contacts.

    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 MYPT1 (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 protein Ser/Thr phosphatase-1 (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 MYPT1 molecule in the predicted complex to that in the target, capri_14_xray.pdb. To compute this angle, we first perform a rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) on the protein Ser/Thr phosphatase-1 (predicted protein Ser/Thr phosphatase-1 onto the target protein Ser/Thr phosphatase-1) 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 MYPT1 and the protein Ser/Thr phosphatase-1 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 T14_P94.1.B.highlighted is illustrated in part:

    Number of Contacts = 112 Matching List1 = 96/157

    B5    ASP - A197  ASP 1
    B6    ALA - A197  ASP 1
    B6    ALA - A198  THR 1
    B9    LYS - A198  THR 1
    B10   ARG - A197  ASP 1
    B10   ARG - A198  THR 1
    B10   ARG - A218  GLU
    B10   ARG - A222  GLY 1
    B10   ARG - A223  VAL 1
    B10   ARG - A224  SER 1
    B10   ARG - A225  PHE 1
    B11   ASN - A225  PHE
    B13   GLN - A177  SER 1
    B13   GLN - A178  PRO 1
    B13   GLN - A179  ASP 1
    B13   GLN - A198  THR 1
    B13   GLN - A199  GLY 1
    B13   GLN - A203  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_14_xray.B.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, T14_P94.1.B.highlighted

    N_res_Ligand = 48 N_res_Receptor = 54 Match Ligand in List1 = 43/76 Matching Receptor in List1 = 53/68

    B5    ASP 1
    B6    ALA 1
    B7    LYS
    B9    LYS 1
    B10   ARG 1
    B11   ASN
    B13   GLN 1
    B14   LEU 1
    . RECEPTOR LIST A21 GLY 1 A22 CYS 1 A23 ARG 1 A24 PRO 1 A70 THR 1 A74 ARG 1 A168 LYS 1

    Each time a residue of the MYPT1 (Ligand) or protein Ser/Thr phosphatase-1 (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_14_xray.B.intres.

    Note that interface residues list files and contact list ones are named the same (i.e. T14_P94.1.B.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 T14_P94.1.B.fitting.summary

    Fitting of A prediction receptor Subunit onto X CAPRI receptor Subunit
    Rotation Matrix:
      -0.03171   0.52998   0.84741
      -0.99722  -0.07393   0.00891
       0.06737  -0.84478   0.53086
      Translation vector     11.961  -210.117  -337.747
    Fitting Ligands, B onto U
    Theta angle = 0.68
    Distance between geometric centres = 0.5091909

    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 MYPT1 and target MYPT1 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 14 evaluation, the first fit was made using the backbones of the common longest fragment between all protein Ser/Thr phosphatase-1 subunits, residues 34,36-38, 41-69, 71-84, 86-143, 145-154, 156-171, 173-195, 197, 199-229, 231-232, 234-236, 239-244, 247-271, 282-2285, 288-293 while the second is made using the common longest fragments of all the MYPT1 subunits, residues 1-290. 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 repector docking are due to the small conformational changes between target Ser/Thr phosphatase-1 and unbound 1FJM (> 2 ┼ ).

    Note that in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri_14_xray.pdb) were renamed as follows:

    A to X
    for Target protein Ser/Thr phosphatase-1 and
    B to U
    for Target MYPT1.


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

    For example part of file cc.T14_P94.1.B.d looks like that:

    Ligand Atom         Receptor Atom           Distance
    B 13   .GLN.NE2     A 179  .ASP.OD1         2.22
    B 264  .VAL.O       A 24   .PRO.CD          2.35
    B 13   .GLN.OE1     A 225  .PHE.CE1         2.37
    B 265  .GLY.O       A 24   .PRO.CD          2.37
    B 38   .PHE.CZ      A 257  .PHE.CE2         2.43
    B 38   .PHE.CD2     A 291  .CYS.CB          2.49

    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.