The evaluation results of the CAPRI Target 19 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_19_xray.A.d:
list of clashes in the interface between ovine prion and Fab antibody subunits.
Final Summary
File
Target 19 Final Summary.
(or use TEXT ONLY version)
summarizes all the information
about the Target 19 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
T19_P12.8.A 0.568 0.343 0.800 0.828 0.769 0.828 959.4 13.4 3.851 6 4.672 1.258
T19_P12.2.A 0.407 0.598 0.800 0.897 0.625 0.839 1164.0 24.2 2.908 6 5.055 2.582
T19_P12.10.A 0.272 0.639 0.720 0.793 0.643 0.821 1008.9 26.0 6.146 6 7.629 2.876
T19_P12.5.A 0.062 0.941 0.840 0.448 0.700 0.433 1023.2 141.9 18.076 15 25.720 9.330
T19_P12.6.A 0.012 0.986 0.720 0.448 0.720 0.433 850.7 140.2 19.986 9 27.386 9.472
T19_P12.9.A 0.012 0.988 0.160 0.655 0.138 0.594 1076.6 101.2 9.169 7 19.485 11.344
.
.
Again T19_P12.8.A means participant 12, prediction 8
for Target 19, Ligand interface B (ovine prion as Ligand and Fab antibody 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 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 ovine prion (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 Fab antibody
(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 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 ovine prion molecule in the predicted complex to that
in the target, capri_19_xray.pdb. To compute this angle,
we first perform a rigid-body fit (Kabsch, 1978, Acta.
Cryst. A. 34, 827-828) on the Fab antibody (predicted Fab antibody onto the
target Fab antibody) 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
ovine prion and the Fab antibody 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.
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
T19_P94.4.A.highlighted is illustrated in part:
HIGHLIGTHED CONTACT LIST FOR T19_P94.4.A
Number of Contacts = 81 Matching List1 = 60/81
A124 GLY - H54 THR 1
A125 LEU - H53 PHE 1
A125 LEU - H54 THR 1
A149 TYR - L53 ARG 1
A153 ASN - L53 ARG 1
A155 TYR - L30A ASP 1
A155 TYR - L30B GLY 1
A155 TYR - L30C LYS 1
A156 ARG - L30C LYS 1
A156 ARG - L49 TYR 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_19_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,
T19_P94.4.A.highlighted
HIGHLIGHTED INTERFACE RESIDUE LIST FOR T19_P94.4.A
N_res_Ligand = 28 N_res_Receptor = 29 Match Ligand in List1 = 24/25 Matching Receptor in List1 = 26/29
LIGAND LIST
A124 GLY 1
A125 LEU 1
A128 TYR
A149 TYR 1
A153 ASN 1
A155 TYR 1
.
.
RECEPTOR LIST
H28 THR 1
L29B ASP 1
L30C LYS 1
L30B GLY 1
L30A ASP 1
L30 SER
H31 ASN 1
.
.
Each time a residue of the ovine prion (Ligand) or Fab antibody (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_19_xray.A.intres.
Note that interface residues list files and contact list
ones are named the same (i.e. T19_P94.4.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
T19_P94.4.A.fitting.summary
Fitting of HL prediction receptor Subunit onto XY CAPRI receptor Subunit
Rotation Matrix:
0.29088 0.95100 0.10480
-0.95627 0.29249 0.00000
-0.03065 -0.10022 0.99449
Translation vector -128.854 -421.276 -46.423
Fitting Ligands, A onto U
Theta angle = 18.67
Distance between geometric centres = 2.860568
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 ovine prion and target ovine prion 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 19 evaluation, the first fit was made
using the backbones of the common longest fragment between all Fab antibody subunits,
residues H2-5, H7-10, H12-24, H26-31, H33-35, H37-35, H37-52, H53-75,
H77-81, L3-28, L31-104 while the second is made using the common longest fragments of all
the ovine prion subunits, residues A132-143, A147-157, A159-169,
A174-175, A177-188, A190-196, A199-207, A210-211. 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 ovine prion
skipps the small conformational changes between unbound 1DWY and target
prions, residues A144-145, A170-173 and A197-198.
Note that in order to not confuse chain ID's between target
and predicted coordinate sets, the chain ID's in the target
(capri_19_xray.pdb) were renamed as follows:
H to X
L to Y
for target Fab antibody and
A to U
for target ovine prion.
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.T19_P94.4.A.d looks
like that:
Ligand Atom Receptor Atom Distance
A 185 .LYS.CE H 53 .PHE.CG 0.78
A 185 .LYS.CE H 53 .PHE.CD1 0.89
--
A 185 .LYS.NZ H 53 .PHE.CD1 1.07
A 188 .THR.CG2 H 31 .ASN.O 1.30
A 196 .GLU.OE1 L 50 .LEU.CG 1.55
A 196 .GLU.OE2 L 49 .TYR.CD1 1.65
A 185 .LYS.CE H 53 .PHE.CB 1.66
.
.
--
A 185 .LYS.CE H 53 .PHE.CD2 2.11
A 197 .ASN.OD1 L 49 .TYR.CG 2.15
A 185 .LYS.CD H 53 .PHE.CG 2.21
A 185 .LYS.CE H 53 .PHE.CE1 2.21
A 193 .THR.O L 96 .GLN.NE2 2.23
.
.
As in the evaluation of target 01, the list of clashes
is segregated into clashes between 0-1, 1-2 and 2-3 Å.
Empty files mean, no close contacts found.
