The evaluation results of the CAPRI TARGET 02 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.
cc.capri.2.DE.d:
list of clashes in the target interface.
In the cc.capri.2.DE.d, file small changes in format
have been introduced relative to the corresponding files
for target 01.
It looks like that:
FAB Atom VP6 Atom Distance
--
--
E 30 .ASP.OD2 C 296 .ARG.NH1 2.29
E 30 .ASP.OD1 C 296 .ARG.NH1 2.47
E 30 .ASP.CG C 296 .ARG.NH1 2.69
D 32 .TYR.CE2 A 174 .ASP.OD2 2.70
E 30 .ASP.O C 300 .MET.N 2.72
D 32 .TYR.CZ A 312 .GLN.NE2 2.76
E 30 .ASP.O C 299 .ASN.CA 2.80
D 32 .TYR.OH A 312 .GLN.NE2 2.89
D 32 .TYR.OH A 174 .ASP.OD2 2.91
The information is split into three columns. Column1 lists
the chain (D and E), residue number and type, and atom name
from of the FAB moiety. Column 2 gives the same information
but for the VP6 , and columne 3 gives the distance in Å.
As for traget 01, the file is divided into three parts
separated by (--) to indicate clashes between 0 -
1 Å (no contacts in this case), between 1 - 2 Å
(none again) and between 2 - 3 Å .
Final Summary
File
Target 02 Final Summary. summarizes all the information
about the target 02 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 VP6 FAB VP6
T02_P26.1.HL 0.000 1.000 0.704 0.000 0.413 0.000 171.0 12.072 46 81.158 39.538
T02_P26.2.HL 0.000 1.000 0.741 0.000 0.556 0.000 141.0 77.382 44 82.241 27.536
T02_P26.3.HL 0.000 1.000 0.852 0.000 0.622 0.000 119.0 106.298 54 109.473 38.779
T02_P26.4.HL 0.000 1.000 0.630 0.000 0.459 0.000 142.2 81.019 36 84.941 27.358
.
.
Again T02_P26.1.HL means participant 26, prediction 1
for the target 02, FAB interface HL (chains H and L). For
all the participants, except for P58, the only interface
with VP6 in their predictions is made by the H and L FAB
subunits (note that H is the same as E and L as D, in capri.2.pdb).
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 fnat.
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, 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 fnon-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.
Columns 4 and 5 list the interface residues ratios over native fIR.
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 VP6
moiety. Note that these ratios are computed considering,
respectively the 3 different FAB/VP6 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 VP6. 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 angle after the second superposition
( see notes for target 01) and column 9 lists the distances,
which this time are the distances between geometric centres
of the predicted and Capri FAB's after first fit ( see Fitting
Summary section) calculated considering FAB chain fragments
that are superimposed in the second fit.
Column 9 lists the number of clashes as defined in the notes
for target 01.
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 VP6's are superimposed L_rmsd. Column 12 contain the rsmd's
when sumperimposing the backbones of the residues at the interface
(FAB + VP6) 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.
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
T02_P27.2.HL.highlighted is illustrated in part:
HIGHLIGTHED CONTACT LIST FOR T02_P27.2.HL
Number of contacts = 61 Matching reference contact list
= 8/52
H27 THR - A244 ALA
H29 THR - A171 PRO
H29 THR - A242 ASP
H29 THR - A244 ALA
H30 ASP - A171 PRO
H30 ASP - A244 ALA
H30 ASP - A245 THR
H30 ASP - C299 ASN*
H30 ASP - C301 THR
H31 TYR - A171 PRO
H31 TYR - C299 ASN*
Each predicted contact that matches the target contact
list is highlighted with "*".
INTERFACE_RESIDUES_HIGHLIGHTED
Directory InterfaceResidues
contains one file per predicted interface, with information
on the residues forming the FAB-VP6 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,
T02_P27.2.HL.highlighted
HIGLIGHTED RESIDUE LIST FOR T02_P27.2.HL
N_res_FAB = 30 N_res_VP6 = 33 Match FAB = 22/27 Match VP6
= 23/27
FAB LIST
H27 THR 10.85123*
H29 THR 32.92757*
H30 ASP 95.48206*
H31 TYR 34.08677*
H32 ALA 42.82428*
H34 HIS 2.907725
H49 VAL 6.581995
H51 SER 27.09415*
H52 PRO 1.703674*
Each time a residue of the FAB or VP6 in the predicted
interface matches one of the interface residues in the target
list, it is highlighted with "*".
Note that interface residues list files and contact list
ones are named the same (i.e. T02_P27.2.HL.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
T02_P27.2.HL.fitting.summary
Fitting of A prediction VP6 subunit onto K capri 2 subunit
Rotation Matrix:
-0.56489 0.55670 0.60908
-0.72701 -0.68493 -0.04823
0.39033 -0.47005 0.79164
Translation vector 48.489 58.269 89.178
Fitting FAB's, HL onto RS
Theta angle = 81.82
Distance between geometric centres = 9.999776
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 VP6
subunit with the highest number of contact vs. any of the VP6
subunits in the target and select the transformation that leaves both the
predicted and target FAB closest as a first fit.
For this target 02 evaluation, the first fit was made
using the backbones of whole VP6 subunits ( in this case
A onto N), while the second fit was made considering the
smallest FAB fragment common to all the participants, e.g.
residues 0-108 for H subunits (E in Capri) and residues
1 - 105 in L subunit (D 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 VP6 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.2pdb) were renamed as follows:
A to K
B to Y
C to N
for the VP6 subunits
D to R
E to S
for the FAB subunits.
FITTED PDB
Directory
FittedPDB contains the files with the coordinates
of the predicted and target complexes superimposed, following
the first fit, in which the VP6 subunits have been superimposed
(using the listed rotation matrix and translation vector).
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.T02_P27.2.HL.d looks
like that:
FAB Atom VP6 Atom Distance
--
H 51 .SER.CB A 171 .PRO.CD 1.40
H 98 .LEU.CD2 C 302 .PRO.CB 1.41
--
H 99A.PHE.CZ C 300 .MET.O 2.45
L 93 .SER.CA A 313 .PRO.CD 2.01
H 51 .SER.CB A 171 .PRO.CG 2.09
L 93 .SER.CB A 313 .PRO.CD 2.19
H 98 .LEU.CG C 302 .PRO.CB 2.21
H 98 .LEU.CD2 C 302 .PRO.CG 2.33
H 51 .SER.CA A 171 .PRO.CG 2.34
L 94 .TYR.OH A 174 .ASP.OD2 2.39
H 51 .SER.OG A 171 .PRO.CD 2.47
L 92 .ALA.O A 313 .PRO.CG 2.54
L 49 .TYR.OH C 310 .ASN.OD1 2.55
H 51 .SER.CA A 171 .PRO.CD 2.56
.
.
.
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.
