capri.3.pdb: the crystal structure of the target (target 03) in PDB format.

cc.capri.3.HL.d: list of clashes in the target HL interface.

File target 03 Final Summary. summarizes all the information about the target 03 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)	THETA ANGLE	DISTANCE		Nclash		L_rmsd		I_rmsd
								   FAB       	HMGL      	   FAB       	HMGL      
   

T03_P26.4.HL		   0.683	   0.494		   0.545	0.824		   0.600	0.737		 20.4		  6.150 	   100  		  7.438 	  1.679
T03_P26.5.HL		   0.016	   0.984		   0.364	0.147		   0.400	0.179		123.7		 40.716 	    44  		 47.340 	 16.448
T03_P26.1.HL		   0.000	   1.000		   0.242	0.000		   0.222	0.000		110.9		 81.086 	    54  		 84.690 	 33.794
T03_P26.2.HL		   0.000	   1.000		   0.333	0.000		   0.500	0.000		 74.5		 83.193 	    62  		 85.180 	 30.837
T03_P26.3.HL		   0.000	   1.000		   0.212	0.000		   0.179	0.000		175.8		 53.365 	    76  		 61.492 	 24.483
.

Again T03_P26.1.HL means participant 26, prediction 1 for the target 03, FAB interface HL (chains H and L). For all the participants, except for P58, the only interface with Hemagglutinin in their predictions is made by the H and L FAB subunits (note that in capri.3.pdb we have H and T, the Fab heavy chains, and L and U, light chains, that are identical in sequence).

In contrast, participant 58 used all three possible FAB pairs (HL, IM and JQ) for their calculations. In the evaluation these interfaces are considered to be independent, and compared separately with the reference. This was done for sake of consistency with the target 01 evaluation methodology.

Column 2 gives the fraction of predicted contacts over native f_nat. 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. In fact we compute 2 different ratios, one for each of the 2 different interfaces in the target and retain the largest ratio for the summary. The contact lists for the target are Contres1 and Contres2. As mentioned above, 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 false positive f_non-nat contact fraction. 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. The number given in this table is the one referred to the target contact list which gives the highest contact ratio over prediction.

Columns 4 and 5 list the interface residues ratios over native f_IR. Column 4 give the ratio between the residues of the FAB that are part of the interface in the prediction, over the FAB residues that are part of the interface in the target. The 5th column gives the same information for the Hemagglutinin moiety. Note that these ratios are computed considering, respectively the 2 different FAB/Hemagglutinin interfaces in the target, but again we list in the summary the results when compared to the target interface which gives the hihgest contact ratio (ON). Column 5, list the interface contact ratio for the Hemagglutinin. All the interface residues lists are generated using the BRUGEL package.

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 rotation angle (Theta angle) necessary to fit the FAB molecule in the predicted complex to that in the target, as per capri.3.pdb. To compute this angle, we first perform a rigid-body fit (Kabsch, 1978, Acta. Cryst. A. 34, 827-828) of the Hemagglutinin subunit in the predicted complex, to the Hemagglutinin subunit in the target. The particular subunits superimposed are listed in the detailed information (see the FITTING_SUMMARY below).

After this first fit, a second fit is performed so as to superimpose the predicted FAB molecules onto its closest counterpart in the target structure (capri.3.pdb closest). The rotation angle corresponding to this second fitting is the listed theta angle. Computed angles and distances are done considering the FAB chain fragments that are sumperimposed in the second fit (see FITTING_SUMMARY section).

Column 9 lists the distance (in Angstroms) between geometric centers of predicted and target FAB 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 FAB in the prediction relative to the position in the target.

Column 10 lists the number clashes N_clash between the FAB and the Hemagglutinins for each predicted complex. Clashes are computed between heavy atom within 3 Å . In the detailed information you can find the clash pairs classified into three categories: from 0 to 1, from 1 to 2 and from 2 to 3 Å.

Columns 11 and 12 list the RMSD's (Root Mean Square Deviation) values in Å . Column 11 list the RMSD values calculated between the FAB's backbones once the Hemagglutinins are superimposed. Column 12 contain the rsmd's when sumperimposing the backbones of the residues at the interface (FAB + Hemagglutinin) on the prediction upon the counterpart in the target I_rmsd. Residues at the interface 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.

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 T03_P26.4.HL.highlighted is illustrated in part:

HIGHLIGTHED CONTACT LIST FOR T03_P26.4.HL.highlighted

Number of contacts = 85 Matching list1 = 43/63 Matching List2 = 39/63

H24  VAL - A160 THR
H25  THR - A160 THR
H26  GLY - A160 THR
H26  GLY - A161 TYR
H26  GLY - A162 PRO	1
H26  GLY - A163 VAL	1
H26  GLY - A197 GLN
H27  TYR - A161 TYR
H27  TYR - A162 PRO	1
H27  TYR - A163 VAL	1	2
H27  TYR - E187 THR

Each predicted contact that matches the target contact list 1 (Contres1) is highlighted with "1" and if it matches contact list 2 (Contres2) is highlighted with "2".

Directory InterfaceResidues contains one file per predicted interface, with information on the residues forming the FAB-Hemagglutinin interface in the prediction and how well they match those in the target interfaces.

The information contained in each file is illustrated by an example, T03_P26.4.HL.highlighted

HLHIGLIGHTED RESIDUE LIST FOR T03_P26.4.HL.highlighted

N_res_FAB = 30 N_res_HMGL = 38 Match HL_FAB = 18/33 Match HL_HMGL = 28/34 Match TU_FAB = 16/32 Match TU_HMGL = 31/35

FAB LIST
 
H2   VAL   18.433	1
H24  VAL    3.365
H25  THR   34.322
H26  GLY   44.707	1	2
H27  TYR   69.739	1	2
H28  SER   50.623	1	2

 
HEMAGGLUTININ LIST
 
A128 THR   76.441	1	2
A129 GLY   30.649	1	2
A157 SER   33.476	2
A158 GLY    7.710	1	2
A159 SER   19.594	1	2
A160 THR   80.965	1

Each time a residue of the FAB or Hemagglutinin in the predicted interface matches one of the interface residues in the target list, it is highlighted with either " 1", "2" or both to indicate which capri T03 interface residue list is matched (1 means capri.3.HL.intres and 2 capri.3.TU.intres).

Note that interface residues list files and contact list ones are named the same (i.e. T03_P26.4.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 T03_P26.4.HL.fitting.summary

Fitting of E prediction HMGL subunit onto W capri 3 subunit
Rotation Matrix:
   0.08318   0.95763   0.27572
   0.33307  -0.28748   0.89801
   0.93923   0.01714  -0.34287
  Translation vector 1.640    83.826   -25.483
Fitting FAB's, HL onto YR
Theta angle = 20.38
Distance between geometric centres = 6.150477

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 FAB and Capri FAB after this first fit and the Theta angle of the second fit. Again we use the optimal fit in the sense that we scan all the possible Hemagglutinin subunit with the highest number of contact vs. any of the Hemagglutinin subunits in the target and select the transformation that leaves both the predicted and target FAB closest as a first fit.

For this target 03 evaluation, the first fit was made using the backbones of whole Hemagglutinin large chains A, C, E (skipping residues 1-8 that appear only in P73 submissions and in orginal unbound 1HGH.pdb) as they are the only ones of the heterodimers (AB,CD,EF) forming Hemagglutinin antigen that are involved in the contacts. Also the rmsd on single unbound - bound large chains are better than the corresponding unbound - bound on small Hemagglutinin chains and than the combination bound - unbound large+small. In this context, the prediction large chain with the highest number of contacts is fitted onto capri large chain with the highest number of contacts at the interface which this prediction scores the best. While the second fit was made considering the smallest FAB fragment common to all the participants, e.g. residues 1-117 for H, I, J subunits (H, T in Capri) and residues 1 - 106 in L,M,Q subunits (L,U in Capri). In order to be consistent, the distance between geometric centres was calculated taking into account only this fragment, which in fact corresponds to the variable domains in contact with the Hemagglutinin protein.

Note that in order to not confuse chain ID's between target and predicted coordinate sets, the chain ID's in the target (capri.3.pdb) were renamed as follows:

A to W
B to K
C to X
D to N
E to O
F to P
for the Hemagglutinin subunits

H to Y
L to R
T to S
U to V
for the FAB subunits.

Directory FittedPDB contains the files with the coordinates of the predicted and target complexes superimposed, following the first fit, in which the Hemagglutinin subunits have been superimposed (using the listed rotation matrix and translation vector). Fitted Pdb are now regenerated according to the new fits.

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

For example part of file cc.T03_P26.4.HL.d looks like that:

FAB Atom        HEMAGGLUTININ Atom    Distance
--
H 107 .PHE.CB 	E 189 .GLN.CG     	1.67
H 107 .PHE.CG 	E 189 .GLN.CG     	1.68
H 107 .PHE.CB 	E 189 .GLN.CD     	1.76
H 107 .PHE.CD2  E 189 .GLN.CB     	1.86
H 107 .PHE.CD2  E 189 .GLN.CG     	1.89
--
H 107 .PHE.O  	E 189 .GLN.NE2    	2.13
H  31 .SER.OG 	A 163 .VAL.O      	2.15
H 107 .PHE.CB 	E 189 .GLN.OE1    	2.17
H 100 .TYR.CB 	E 189 .GLN.OE1    	2.19

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As in the evaluation of target 01, the list of clashes is segregated into contacts between 0-1 (no contacts in this example), 1-2 and 2-3Å.