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

Rank of the prediction among all predictions submitted on the selected target according to the GDT_TS score.

Model

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

Gr#

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 server-CASP experiment.

Group_pred

Name of the predicting group.

Charts

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:
|Ti-Mi|< 1 Å: CYAN
|Ti-Mi|< 2 Å: GREEN
|Ti-Mi| < 4 Å: YELLOW
|Ti-Mi| < 8 Å: ORANGE
|Ti-Mi| > 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 Target-Model 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

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_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

GDC_SC - Global Distance Calculation for sidechains
GDC_SC is GDT-like metrics wich uses a characteristic atom near the end of each sidechain type (instead of CA's) for the evaluation of residue-residue distance deviations.
GDC_SC = 2*(k*GDC_P1 + (k-1)*GDC_P2 ... + 1*GDC_Pk)/(k+1)*k, k=10
where GDC_Pk denotes percent of residues under distance cutoff <= 0.5kÅ

GDC_ALL

GDC_ALL - Global Distance Calculation for all atoms
GDC_ALL = 2*(k*GDC_P1 + (k-1)*GDC_P2 ... + 1*GDC_Pk)/(k+1)*k, k=10
where GDC_Pk denotes percent of atoms under distance cutoff <= 0.5kÅ

Z-M1-GDT

Z-M1-GDT (applicable to models No.1 only) - z-score 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).

Z-M1s-GDT

Z-M1s-GDT (applicable to models No.1 and server groups only) - z-score showing relative quality of the model among the first models submitted on the target by server groups (based on the GDT_TS score).

Z-MA-GDT

Z-MA-GDT - z-score 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).

Z-MAs-GDT

Z-MAs-GDT (applicable to server groups only) - z-score showing relative quality of the model among all models submitted on the target by server groups (based on the GDT_TS score).

RMS_CA

RMS_CA - Root-mean-square deviation for the entire target structure or a subdomain, calculated on CA atoms and based on a sequence-dependent superposition.

RMS_ALL

RMS_ALL - Root-mean-square deviation for the entire target structure or a subdomain, calculated on all atoms and based on a sequence-dependent superposition.

RMSD

RMSD - Root-mean-square deviation for the subset of CA atoms from the model that correspond to the residues from target structure or a subdomain in the sequence-independent LGA superposition.

NP

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.

NT

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.

NM

Number of residues in model.

NP_P

NP_P = NP / NT * 100% - percent of residues predicted in the model from among those possible to evaluate.

AP_P

Percent of non-hydrogen atoms predicted in the model from among those possible to evaluate.

err

Total number of CA-CA irregularities in the prediction. Irregularity is reported if
0.1Å<|CAi-CAj|<3.6Å  or   |CAi-CAi-1|>4.0Å.
Very closely located CA atoms (|CAi-CAj|<0.1Å) are not included into the total number of irregularities.
Detailed analysis of CA-CA irregularities can be found on the GDT pages.

CACA-mean

Mean distance between consecutive CA atoms in the model.

CACA-std_dev

Standard deviation of distances between consecutive CA atoms in the model.

PC01

This column contains results of rmsd-based 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

PC05

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_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

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_P = AL4 / NT * 100% - percent of residues that can be correctly aligned with allowance for 1-4 -residue shift based on the LGA sequence independent superposition generated with a 4Å distance cutoff.

AL4

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_P = ALI / NT * 100% - percent of residues that can be correctly structurally aligned with allowance for more than 4-residue shift based on the LGA sequence independent superposition generated with a 4Å distance cutoff.

Z-M1-AL0_P

Z-M1-GDT (applicable to models No.1 only) - z-score 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).

Z-M1s-AL0_P

Z-M1s-GDT (applicable to models No.1 and server groups only) - z-score showing relative quality of the model among the first models submitted on the target by server groups (based on the AL0_P score).

Z-MA-AL0_P

Z-MA-GDT - z-score 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).

Z-MAs-AL0_P

Z-MAs-GDT (applicable to server groups only) - z-score showing relative quality of the model among all models submitted on the target by server groups (based on the AL0_P score).

ALI

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

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

EQV5_4 = EQ4 / NT * 100% - percent of residues that can be correctly aligned with allowance for 1-4 -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

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 Z-Score

ProSA uses knowledge-based potentials of CA atoms. (ref.: ProSA web:...)
The Z-Score 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.

MP-Score

Aggregated Molprobity Score calculated according to the formula:
MP-Score = 0.426 *ln(1 + Clash-Score) + 0.33 *ln(1 + max(0, Rot-out - 1)) + 0.25 *ln( 1 + max(0, (100 - Ram-fv) - 2 )) + 0.5

Clash-Score

Molprobity Clash Score - the number of all-atom steric overlaps > 0.4Å per 1000 atoms.

Rot-out

Molprobity Rotamer Outliers Score - percentage of sidechains conformations classified as rotamer outliers, from those sidechains that can be evaluated.

Ram-out

Molprobity Ramachandran Outliers Score - percentage of backbone Ramachandran conformations classified as outliers.

Ram-fv

Molprobity Ramachandran Favored Score - percentage of backbone Ramachandran conformations in favored region.

SG

The average value of Sphere Grinder Score calculated for two sets of parameters: spheres' radii = 6Å in both cases and RMSD-cutoffs = 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.

Global lDDT score

The lDDT score is computed by comparing inter-atomic interactions in models and targets. (ref.:CASP9 TBM Assessment)

CAD score

CAD-score evaluates protein models against the target stucture by quantifying differences between contact areas.
(ref.: CAD-score:...)
AA - all atoms are calculated;
SS - atoms of sidechains are taken into account only

RPF

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 F2-measure are calculated accordingly. A F2-measure score for a random structure is also calculated. The RPF score is a normalized F2-measure score where RPF(random) = 0 and RPF(Target) = 1.
Dmax = 9Å.

QCS

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 C-alpha contacts. (ref.: An automatic method ...)

ContS

Contact score based on all C-alpha from QCS bundle.

SOV

SOV score measures the correctness of secondary structure predictions.
The CASP TS predictions are translated into SS predictions by dssp.
(ref:sov_help)

TMscore

TMscore measures the similarity of two protein structures.
(ref:Scoring function for ...)

CE

CE (Combinatorial Extension) is a method for comparing and aligning protein structures.
(ref:Protein structure alignment ...)

DFM

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 template-free ...)

Handedness

Handedness score is calculated as a fraction of the same-way oriented tetrahedrons with vertices at C-alpha's
at target and model structures in the procedure of randomly selecting atoms and repeating 50,000 times.
(ref:Assessment of template-free ...)

CoDM

CoDM score is a weighted Pearson's correlation of the distance matrices of the target and model structures.
(ref:Assessment of template-free ...)

FlexE

The score is based on the energy of elastic deformation between two structures: model and target.
(ref:FlexE: Using Elasic Network Models to ...)

ASE

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(tfi/d0)-S(di/d0)|))
where tfi - temperature factor of the i-th residue in the model
di - distance between i-th residues in lga alignment (sequence dependent mode)
S(x) = 1/(1+x^2) - S-function
d0 - scaling factor, set d0=5.0

Pclust

Column "Pclust" contains 2 values showing results of rmsd-based 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                     

CA-CA_irreg

Format of the column:

                                10/3-40(2)
                                |  |  | |
                                |  |  | C4: Number of clusters of identical CA atoms
C1: Number of CA-CA irregularities |  |
                                   |  C3: Total number of identical CA atoms
     C2: Number of severe collisions

C1 (0.1Å<|CAi-CAj|<3.6Å or <|CAi-CAi-1|>4.0Å)
CA-CA irregularity is reported if
Very closely located CA atoms (|CAi-CAj|<0.1Å) are not included into the total number of irregularities C1 and are counted separately (C3).
C2 (0.1Å<|CAi-CAj|<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 (|CAi-CAj|<0.1Å) are not included into the total number of severe collisions C2 and are counted separately (C3).
C3 (|CAi-CAj|<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 non-zero entries in the "CA-CA_irreg" column points to the detailed information about CA-CA clashes in the prediction.
Format:

50     51     13.40
#res1  #res2  distance(Å)


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