The evaluation results of the CAPRI Target 13 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_13_xray.AB.d:
list of clashes in the interface between antibody and SAG1 subunits.
Final Summary
File
Target 13 Final Summary. summarizes all the information
about the Target 13 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
T13_P01.7.HL 0.114 0.877 0.688 0.280 0.611 0.219 864.5 139.7 32.276 46 42.407 5.574
T13_P01.5.HL 0.043 0.961 0.875 0.360 0.718 0.310 839.6 104.6 30.386 46 37.747 6.622
T13_P01.1.HL 0.000 1.000 0.781 0.000 0.862 0.000 821.4 139.2 63.939 69 69.145 12.284
T13_P01.10.HL 0.000 1.000 0.688 0.040 0.595 0.032 822.8 108.3 48.946 37 52.837 11.006
T13_P01.2.HL 0.000 1.000 0.625 0.000 0.645 0.000 888.9 46.3 46.466 42 47.400 12.422
.
.
Again T13_P01.7.HL means participant 01, prediction 7
for the Target 13, Ligand interface HL (antibody as Ligand and SAG1 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.
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 antibody (Ligand) that
are part of the interface in the prediction, over the
the residues in the equivalent subunits in the target that are part of the interface in the target.
The 5th column gives the same information for the residues in the SAG1
(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 antibody molecule in the predicted complex to that
in the target, as for capri_13_xray.pdb. To compute this angle,
we first perform a rigid-body fit (Kabsch, 1978, Acta.
Cryst. A. 34, 827-828) on the SAG1 (predicted SAG1 onto the
target SAG1) 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
antibody and the SAG1 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.
Note that for participant P12, predictions 1-3,6-8 the
Interface RMSD's couldn't be calculated because coordinates for the corresponding
N-terminal fragment on the SAG1 molecules were not provided.
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
T13_P02.5.HL.highlighted is illustrated in part:
HIGHLIGTHED CONTACT LIST FOR T13_P02.5.HL
Number of Contacts = 83 Matching List1 = 53/70
H28 ASP - A37 THR 1
H29 ILE - A37 THR
H30 SER - A36 LYS
H30 SER - A37 THR 1
H30 SER - A115 LYS
H31 ASN - A37 THR
H31 ASN - A115 LYS
H32 TYR - A37 THR 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_13_xray.AB.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,
T13_P02.5.HL.highlighted
HIGHLIGHTED INTERFACE RESIDUE LIST FOR T13_P02.5.HL
N_res_Ligand = 34 N_res_Receptor = 27 Match Ligand in List1 = 29/32 Matching Receptor in List1 = 22/25
LIGAND LIST
H28 ASP 1
H29 ILE
H30 SER 1
H31 ASN 1
H32 TYR 1
H49 TYR
H50 TYR 1
.
.
L530 THR 1
L531 ASP 1
L532 TYR 1
L533 GLY 1
L550 ILE 1
.
.
RECEPTOR LIST
A14 ASP
A36 LYS 1
A37 THR 1
A38 ALA 1
A39 LEU 1
.
.
Each time a residue of the antibody (Ligand) or SAG1 (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_13_xray.AB.intres.
Note that interface residues list files and contact list
ones are named the same (i.e. T13_P02.5.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
T13_P02.5.HL.fitting.summary
Fitting of A prediction receptor Subunit onto X CAPRI receptor Subunit
Rotation Matrix:
0.98293 0.01718 -0.18318
0.00923 0.98977 0.14234
0.18376 -0.14160 0.97272
Translation vector 27.909 -6.173 52.148
Fitting Ligands, HL onto UV
Theta angle = 13.42
Distance between geometric centres = 4.569442
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 antibody and target antibody 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 13 evaluation, the first fit was made
using the backbones of the common longest fragment between all SAG1 subunits,
residues 2009-2012, 2017-2028, 2030-2035, 2039-2040, 2093-2098, 2104-2111, 2113-2117,
2122-2130; while the second is made using the commong longest
fragments of all the dockering subunits, residues 7-9, 19, 39, 41, 68, 70, 73
76, 82, 97, 101 in chain A and residues 501-534, 536-540, 542-614 in
chain B. In order to be consistent,
the distance between geometric centres was calculated taking
into account only this ligand fragment.
Note that there is a big hinge affecting D2 domain residues from 121 on in
the SAG1 molecule upon binding, which is not taken into account for the fittings.
Note that in order to not confuse chain ID's between target
and predicted coordinate sets, the chain ID's in the target
(capri_13_xray.pdb) were renamed as follows:
F to X
for the target SAG1 and
A to U
B to V
for the target antibody.
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.T13_P02.5.HL.d looks
like that:
Ligand Atom Receptor Atom Distance
--
L 602 .TRP.CE2 A 43 .PRO.CD 1.26
L 602 .TRP.NE1 A 43 .PRO.CD 1.72
L 602 .TRP.CG A 43 .PRO.CG 1.83
L 600 .SER.O A 63 .THR.OG1 1.91
L 602 .TRP.CD2 A 43 .PRO.CG 1.93
L 602 .TRP.CD2 A 43 .PRO.CD 1.94
L 602 .TRP.CZ2 A 43 .PRO.CD 1.96
--
L 602 .TRP.CD1 A 43 .PRO.CG 2.07
H 30 .SER.CB A 37 .THR.OG1 2.15
L 601 .THR.CG2 A 118 .ASP.OD1 2.16
L 557 .ASP.OD1 A 52 .GLN.OE1 2.18
.
.
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.
Empty files means, no close contacts found.
