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.
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 5Å 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 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 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 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
T14_P94.1.B.highlighted is illustrated in part:
HIGHLIGTHED CONTACT LIST FOR T14_P94.1.B
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.
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,
T14_P94.1.B.highlighted
HIGHLIGHTED INTERFACE RESIDUE LIST FOR T14_P94.1.B
N_res_Ligand = 48 N_res_Receptor = 54 Match Ligand in List1 = 43/76 Matching Receptor in List1 = 53/68
LIGAND LIST
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.
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
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 Å ).
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.
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.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 2-3Å.
Empty files mean, no close contacts found.
