Results Table HELP
Consecutive number of the prediction in the table ordered by the selected
column. To sort results by the selected column click on the small triangle
next to the column title. Results in the sorted column are bolded.
Rank of the prediction among all predictions submitted on the selected
target according to the GDT_TS score.
Name of the model as assigned at the time of prediction acceptance.
Name of each model is composed from the number of the target,
prediction format category, prediction group number, and model index.
If a model has more than one independent segment they are in separate files
with additional index indicating their sequential position within the
model.
Letter 'u' appended to the index of model or independent
segment indicates UNREFINED set of coordinates.
Example:
Model name T0201TS012_2u has the following components:
T0201 target number
TS Tertiary Structure (3D atoms coordinates) prediction
012 prediction group 12
2u model index 2, UNREFINED set of coordinates
Number of the predicting group received at the registration. Letter "s" placed
next to the group number identifies the group as taking part in the serverCASP
experiment.
Name of the predicting group.
A

Flat text file (output from
ACE
program) and LGA which contains
most of the numerical data available through this browser.

D

Target and model structures superimposed in sequence dependent manner.
Only CA atom pairs closer than 4.0 Å were used to obtain this
superposition. The GDT procedure was used to select the set of CA atom pairs.
Coloring scheme is based on distances between corresponding residues:
TiMi< 1 Å: CYAN
TiMi< 2 Å: GREEN
TiMi < 4 Å: YELLOW
TiMi < 8 Å: ORANGE
TiMi > 8 Å: PURPLE for target, RED for model

I

Target and model structures superimposed in sequence independent manner.
This superposition was generated using
LGA
structural alignment, i.e.
completely ignoring sequence relationship between target and model.
Coloring scheme is based on alignment accuracy for corresponding residues:
perfectly aligned: GREEN
within 4 residues: YELLOW
not aligned: PURPLE for target, RED for model
Note: Structural superposition is not shown when
model had less than 10 residues.

G

Plot shows TargetModel
GDT (Global Distance Test) results.

Superimposed target and model structures are provided as Rasmol scripts.
To make use of these scripts you should have Rasmol installed locally.
If you don't know how to configure your browser to display Rasmol scripts,
please read the instructions.
GDT_TS  GlobalDistanceTest_TotalScore
GDT_TS = (GDT_P1 + GDT_P2 + GDT_P4 + GDT_P8)/4,
where GDT_Pn denotes percent of residues under distance cutoff <= nÅ
GDT_HA  GDT High Accuracy
GDT_HA = (GDT_P0.5 + GDT_P1 + GDT_P2 + GDT_P4)/4,
where GDT_Pn denotes percent of residues under distance cutoff <= nÅ
GDC_SC  Global Distance Calculation for sidechains
GDC_SC is GDTlike metrics wich uses a characteristic atom near the end of
each sidechain type (instead of CA's) for the evaluation of residueresidue
distance deviations.
GDC_SC = 2*(k*GDC_P1 + (k1)*GDC_P2 ... + 1*GDC_Pk)/(k+1)*k, k=10
where GDC_Pk denotes percent of residues under distance cutoff <= 0.5kÅ
GDC_ALL  Global Distance Calculation for all atoms
GDC_ALL = 2*(k*GDC_P1 + (k1)*GDC_P2 ... + 1*GDC_Pk)/(k+1)*k, k=10
where GDC_Pk denotes percent of atoms under distance cutoff <= 0.5kÅ
ZM1GDT (applicable to models No.1 only)  zscore showing relative quality
of the model among the first models submitted on the target by both human and server
groups (based on the GDT_TS score).
ZM1sGDT (applicable to models No.1 and server groups only)  zscore showing relative quality
of the model among the first models submitted on the target by server groups (based on the GDT_TS score).
ZMAGDT  zscore showing relative quality of the model among all models submitted on the target
by both human and server groups (based on the GDT_TS score).
ZMAsGDT (applicable to server groups only)  zscore showing relative quality of the model among
all models submitted on the target by server groups (based on the GDT_TS score).
RMS_CA  Rootmeansquare deviation for the entire target structure or a subdomain, calculated on CA atoms and based on a sequencedependent superposition.
RMS_ALL  Rootmeansquare deviation for the entire target structure or a subdomain, calculated on all atoms and based on a sequencedependent superposition.
RMSD  Rootmeansquare deviation for the subset of CA atoms from the model that correspond to the residues from target structure or a subdomain in the sequenceindependent LGA superposition.
Number of residues in a prediction submitted on the target or a subdomain.
This is a subset of residues in the prediction that overlap by sequence with the residues
possible to evaluate for that target/domain.
Number of residues in target (as received from experimentalists) or a subdomain
(as defined by assessors). In other words, number of residues possible to evaluate.
Number of residues in model.
NP_P = NP / NT * 100%  percent of residues predicted in the model from among those possible to evaluate.
Percent of nonhydrogen atoms predicted in the model from among those possible to evaluate.
Total number of CACA irregularities in the prediction.
Irregularity is reported if
0.1Å<CA_{i}CA_{j}<3.6Å or
CA_{i}CA_{i1}>4.0Å.
Very closely located CA atoms (CA_{i}CA_{j}<0.1Å)
are not included into the total number of irregularities.
Detailed analysis of CACA irregularities can be found on the GDT pages.
Mean distance between consecutive CA atoms in the model.
Standard deviation of distances between consecutive CA atoms in the model.
This column contains results of rmsdbased clustering of predictions and reports number of predictions that are similar to the model (RMSD < 0.1Å).
Data numbers are links that lead to the model names that are similar to the current prediction.
Format of the record:
T0199TS033_4: 2: 164_1 352_4
  
Model  ____ Shortened names of similar predictions.
Number of 164_1 corresponds to T0199TS164_1 or T0199AL164_1
similar predictions
Number of other predictions that are similar to the model (RMSD < 0.5Å).
Data numbers are links that lead to the model names that are similar to the current prediction. Format of the record is the same as for PC01 (see above).
AL0_P = AL0 / NT * 100%  percent of residues correctly aligned in the model (from among those possible to evaluate) based on the LGA sequence independent superposition generated with a 4Å
distance cutoff.
AL0: Number of correctly aligned residues in the 4Å LGA superposition of the model and experimental structure of the target. A model residue is considered to be correctly aligned if the CA atom falls within 3.8Å of the corresponding experimental atom, and there is no other experimental structure CA atom nearer.
AL4_P = AL4 / NT * 100%  percent of residues that can be correctly aligned with allowance for 14 residue shift based on the LGA sequence independent superposition generated with a 4Å distance cutoff.
AL4: Number of residues in the model for which the closest experimental structure CA atom is within +/4 residues of the correct one, and the distance between the corresponding residues is less than 3.8Å (based on the LGA sequence independent superposition generated with a 4Å distance cutoff).
ALI_P = ALI / NT * 100%  percent of residues that can be correctly structurally aligned with allowance for more than 4residue shift based on the LGA sequence independent superposition generated with a 4Å distance cutoff.
ZM1GDT (applicable to models No.1 only)  zscore showing relative quality
of the model among the first models submitted on the target by both human and server
groups (based on the AL0_P score).
ZM1sGDT (applicable to models No.1 and server groups only)  zscore showing relative quality
of the model among the first models submitted on the target by server groups (based on the AL0_P score).
ZMAGDT  zscore showing relative quality of the model among all models submitted on the target
by both human and server groups (based on the AL0_P score).
ZMAsGDT (applicable to server groups only)  zscore showing relative quality of the model among
all models submitted on the target by server groups (based on the AL0_P score).
ALI: Number of residues in the model for which there exists an aligned residue in the target structure located less than 3.8Å apart (based on the LGA sequence independent superposition generated with a 4Å distance cutoff).
EQV5_0  percent of residues correctly aligned in the model (from among those NT possible to evaluate) based on the sequence independent superposition generated with a 4Å distance cutoff. A residue is assumed to be correctly aligned if a corresponding experimental structure residue in the LGA alignment is also the correct one on the sequence, and the distance between them is less than 4Å .
EQV5_4 = EQ4 / NT * 100%  percent of residues that can be correctly aligned with allowance for 14 residue shift based on the sequence independent superposition generated with a 4Å distance cutoff.
EQ4: Number of residues in the model for which corresponding residue in the LGA alignment output is within +/4 residues of the correct one, and the distance between the corresponding residues is less than 4Å .
EQV5_I = EQI / NT * 100%  percent of residues that can be correctly structurally aligned with allowance for any residue shift based on sequence independent superposition generated with a 4Å distance cutoff.
EQI: Number of residues in the model for which there exists a corresponding residue in the LGA alignment output and the distance between the corresponding residues is less than 4Å .
ProSA uses knowledgebased potentials of CA atoms. (ref.: ProSA web:...)
The ZScore indicates overall model quality and measures the deviation of the total energy of the structure with respect to an energy distribution derived from random conformations.
Aggregated Molprobity Score calculated according to the formula:
MPScore = 0.426 *ln(1 + ClashScore) + 0.33 *ln(1 + max(0, Rotout  1)) + 0.25 *ln( 1 + max(0, (100  Ramfv)  2 )) + 0.5
Molprobity Clash Score  the number of allatom steric overlaps > 0.4Å per 1000 atoms.
Molprobity Rotamer Outliers Score  percentage of sidechains conformations classified as rotamer outliers, from those sidechains that can be evaluated.
Molprobity Ramachandran Outliers Score  percentage of backbone Ramachandran conformations classified as outliers.
Molprobity Ramachandran Favored Score  percentage of backbone Ramachandran conformations in favored region.
The average value of Sphere Grinder Score calculated for two sets of parameters: spheres' radii = 6Å in both cases and RMSDcutoffs = 2Å and 4Å.
For every residue RMSD between the model and the target is calculated on the set of atoms inside the sphere of a certain radius with the center at CA.
The Sphere Grinder Score (SG)  percentage of residues with RMSD under the cutoff.
The lDDT score is computed by comparing interatomic interactions in models and targets.
(ref.:CASP9 TBM Assessment)
CADscore evaluates protein models against the target stucture by quantifying differences between contact areas.
(ref.: CADscore:...)
AA  all atoms are calculated;
SS  atoms of sidechains are taken into account only
Distances between all N/C atoms within Dmax are computed for both the
Target and Model structures. Atom pairs within Dmax in both structures
are counted as TP. Atom pairs which is less than Dmax in the Target
structure, but greater than Dmax in the Model structures are counted
as FN. Atom pairs which is greater than Dmax in the Target structure,
but less than Dmax in the Model structure are counted as FP. Recall,
Precision and F2measure are calculated accordingly. A F2measure
score for a random structure is also calculated. The RPF score is a
normalized F2measure score where RPF(random) = 0 and RPF(Target) = 1.
Dmax = 9Å.
Quality Control Score (QCS) is a method to evaluate the quality of
structure predictions, especially for template free structure prediction.
It measures and scores correctness of secondary structure elements (SSE) predictions,
their relative positions, handedness of SSE triplets, all Calpha contacts.
(ref.: An automatic method ...)
Contact score based on all Calpha from QCS bundle.
SOV score measures the correctness of secondary structure predictions.
The CASP TS predictions are translated into SS predictions by dssp.
(ref:sov_help)
TMscore measures the similarity of two protein structures.
(ref:Scoring function for ...)
CE (Combinatorial Extension) is a method for comparing and aligning protein structures.
(ref:Protein structure alignment ...)
DFM (deformation score) is calculated as a measure of distortion of correspondinf tetrahedrons
with vertices at atoms at target and model structures.
(ref:Assessment of templatefree ...)
Handedness score is calculated as a fraction of the sameway oriented tetrahedrons with vertices at Calpha's
at target and model structures in the procedure of randomly selecting atoms and repeating 50,000 times.
(ref:Assessment of templatefree ...)
CoDM score is a weighted Pearson's correlation of the distance matrices of the target and model structures.
(ref:Assessment of templatefree ...)
The score is based on the energy of elastic deformation between two structures: model and target.
(ref:FlexE: Using Elasic Network Models to ...)
ASE (Accuracy Self Estimate) score is based on the accuracy of every residue position in the model reported in the temperature factor field.
The ASE score is calculated by formula:
ASE = 100.0*(1  Mean(S(tf_{i}/d_{0})S(d_{i}/d_{0})))
where tf_{i}  temperature factor of the ith residue in the model
d_{i}  distance between ith residues in lga alignment (sequence dependent mode)
S(x) = 1/(1+x^2)  Sfunction
d_{0}  scaling factor, set d_{0}=5.0
Column "Pclust" contains 2 values showing results of rmsdbased clustering of predictions. First column (0.1) reports number of predictions that are very similar to each other (RMSD < 0.1Å). Second column (0.5) shows number of predictions that are similar within the range of 0.5Å. In both cases links lead to the model names that are similar to the current prediction.
Format of the record:
T0199TS033_4: 2: 164_1 352_4
  
Model  ____ Shortened names of similar predictions.
Number of 164_1 corresponds to T0199TS164_1 or T0199AL164_1
similar predictions
Format of the column:
10/340(2)
   
   C4: Number of clusters of identical CA atoms
C1: Number of CACA irregularities  
 C3: Total number of identical CA atoms
C2: Number of severe collisions
C1 (0.1Å<CA_{i}CA_{j}<3.6Å or
<CA_{i}CA_{i1}>4.0Å)
CACA irregularity is reported if

distance between any two CA atoms in the prediction is smaller than 3.6Å

or distance between the two consecutive CA atoms is bigger than 4.0Å.
Very closely located CA atoms (CA_{i}CA_{j}<0.1Å)
are not included into the total number of irregularities C1 and are
counted separately (C3).
C2 (0.1Å<CA_{i}CA_{j}<1.9Å)
Severe collisions are reported if distance between any two CA atoms is less
then twice as short as the regular distance between two consecutive CAs.
Very closely located CA atoms (CA_{i}CA_{j}<0.1Å)
are not included into the total number of severe collisions C2 and are
counted separately (C3).
C3 (CA_{i}CA_{j}<0.1Å)
C3 represents the total number of very closely located CA atoms in the prediction.
These atoms may belong to different clusters of identical atoms (C4).
For example, the prediction that contains 3 identical CA atoms
ATOM 441 CA SER 51 0.000 0.000 0.000 1.00 0.00
ATOM 446 CA ALA 52 0.000 0.000 0.000 1.00 0.00
ATOM 451 CA SER 53 0.000 0.000 0.000 1.00 0.00
and 2 CA atoms with identical coordinates but different from the first group
ATOM 1441 CA SER 251 1.000 2.000 3.000 1.00 0.00
ATOM 1446 CA ALA 252 1.000 2.000 3.000 1.00 0.00
will be assigned number 5 (3+2) as C3 and 2 (different clusters) as C4.
C4
C4 shows how many different clusters very closely located CA atoms
belong to (see explanation for C3).

The hyperlink for nonzero entries in the "CACA_irreg" column points
to the detailed information about CACA clashes in the prediction.
Format:
50 51 13.40
#res1 #res2 distance(Å)
Protein Structure Prediction Center