Results for Example Data

Thu Oct 25 13:36:16 UTC 2018

2F8A

CRYSTAL STRUCTURE OF THE SELENOCYSTEINE TO GLYCINE MUTANT OF HUMAN GLUTATHIONE PEROXIDASE 1

Size: 370 predicted GDT: 72.31 Z-score: 1.5 TM-score: 0.81

Global Quality Assessmenti

eQuant predicts local per-residue deviations between processed structure model and unknown native structure, which are eventually processed further to assess global quality. This overall quality is expressed by means of the global distance test (GDT, [Kryshtafovych, 2014]) score, which is here utilized to quantify the predicted degree of structural deviation between the processed structure model and the unknown native structure. A GDT score of 100% indicates a perfect match.

The blue line shown in this figure illustrates the GDT score of your model. The box plot also shown here characterizes the distribution of pre-processed GDT scores generated by eQuant for a data set of protein structure chains with similar sequence length (± 10% relative length) to your uploaded model. Furthermore, the relation between your GDT score and the mean of pre-processed scores is expressed by a Z-score. Values significantly below the median of the box plot (respectively high Z-score) indicate for good global structure quality.

Protein Vieweri

The structure visualized by PV [Biasini, 2014].

A coloring range of 1 to 7 Å is applied: high quality scores close to 1 are depicted as blue, while regions exhibiting a high amount of local discrepancies are rendered red. Amino acids of mediocre quality are colored white.

Hover over data points in the line chart to highlight that particular amino acid. Click on it to center the view on that residue. While pressing 'Shift' you can translate the point of view. Hit 'Escape' or click the background to restore the initial view.

Local Quality Assessmenti

Analogically with the global quality score, the local quality can be quantified by the comparison with the unknown native conformation of the protein. This time though, the distance between corresponding residues is predicted.

Amino acids in the compact, hydrophobic core will likely exhibit small deviations from the native structure, whereas especially coils exposed to the solvent are prone to spatiotemporal displacement and in consequence to serious disagreements. For each amino acid of this chain the predicted distance is plotted on the y-axis. Residues with distances exceeding 3.8 Å (shaded red) indicate local discrepancies.

2I4A

CRYSTAL STRUCTURE OF THIOREDOXIN FROM THE ACIDOPHILE ACETOBACTER ACETI

Size: 107 predicted GDT: 83.19 Z-score: 3.85 TM-score: 0.58

Global Quality Assessmenti

eQuant predicts local per-residue deviations between processed structure model and unknown native structure, which are eventually processed further to assess global quality. This overall quality is expressed by means of the global distance test (GDT, [Kryshtafovych, 2014]) score, which is here utilized to quantify the predicted degree of structural deviation between the processed structure model and the unknown native structure. A GDT score of 100% indicates a perfect match.

The blue line shown in this figure illustrates the GDT score of your model. The box plot also shown here characterizes the distribution of pre-processed GDT scores generated by eQuant for a data set of protein structure chains with similar sequence length (± 10% relative length) to your uploaded model. Furthermore, the relation between your GDT score and the mean of pre-processed scores is expressed by a Z-score. Values significantly below the median of the box plot (respectively high Z-score) indicate for good global structure quality.

Protein Vieweri

The structure visualized by PV [Biasini, 2014].

A coloring range of 1 to 7 Å is applied: high quality scores close to 1 are depicted as blue, while regions exhibiting a high amount of local discrepancies are rendered red. Amino acids of mediocre quality are colored white.

Hover over data points in the line chart to highlight that particular amino acid. Click on it to center the view on that residue. While pressing 'Shift' you can translate the point of view. Hit 'Escape' or click the background to restore the initial view.

Local Quality Assessmenti

Analogically with the global quality score, the local quality can be quantified by the comparison with the unknown native conformation of the protein. This time though, the distance between corresponding residues is predicted.

Amino acids in the compact, hydrophobic core will likely exhibit small deviations from the native structure, whereas especially coils exposed to the solvent are prone to spatiotemporal displacement and in consequence to serious disagreements. For each amino acid of this chain the predicted distance is plotted on the y-axis. Residues with distances exceeding 3.8 Å (shaded red) indicate local discrepancies.

1VL9

ATOMIC RESOLUTION (0.97A) STRUCTURE OF THE TRIPLE MUTANT (K53,56,121M) OF BOVINE PANCREATIC PHOSPHOLIPASE A2

Size: 123 predicted GDT: 63.03 Z-score: 0.82 TM-score: 0.48

Global Quality Assessmenti

eQuant predicts local per-residue deviations between processed structure model and unknown native structure, which are eventually processed further to assess global quality. This overall quality is expressed by means of the global distance test (GDT, [Kryshtafovych, 2014]) score, which is here utilized to quantify the predicted degree of structural deviation between the processed structure model and the unknown native structure. A GDT score of 100% indicates a perfect match.

The blue line shown in this figure illustrates the GDT score of your model. The box plot also shown here characterizes the distribution of pre-processed GDT scores generated by eQuant for a data set of protein structure chains with similar sequence length (± 10% relative length) to your uploaded model. Furthermore, the relation between your GDT score and the mean of pre-processed scores is expressed by a Z-score. Values significantly below the median of the box plot (respectively high Z-score) indicate for good global structure quality.

Protein Vieweri

The structure visualized by PV [Biasini, 2014].

A coloring range of 1 to 7 Å is applied: high quality scores close to 1 are depicted as blue, while regions exhibiting a high amount of local discrepancies are rendered red. Amino acids of mediocre quality are colored white.

Hover over data points in the line chart to highlight that particular amino acid. Click on it to center the view on that residue. While pressing 'Shift' you can translate the point of view. Hit 'Escape' or click the background to restore the initial view.

Local Quality Assessmenti

Analogically with the global quality score, the local quality can be quantified by the comparison with the unknown native conformation of the protein. This time though, the distance between corresponding residues is predicted.

Amino acids in the compact, hydrophobic core will likely exhibit small deviations from the native structure, whereas especially coils exposed to the solvent are prone to spatiotemporal displacement and in consequence to serious disagreements. For each amino acid of this chain the predicted distance is plotted on the y-axis. Residues with distances exceeding 3.8 Å (shaded red) indicate local discrepancies.

2PNE

CRYSTAL STRUCTURE OF THE SNOW FLEA ANTIFREEZE PROTEIN

Size: 81 predicted GDT: 52.92 Z-score: -1.98 TM-score: 0.31

Global Quality Assessmenti

eQuant predicts local per-residue deviations between processed structure model and unknown native structure, which are eventually processed further to assess global quality. This overall quality is expressed by means of the global distance test (GDT, [Kryshtafovych, 2014]) score, which is here utilized to quantify the predicted degree of structural deviation between the processed structure model and the unknown native structure. A GDT score of 100% indicates a perfect match.

The blue line shown in this figure illustrates the GDT score of your model. The box plot also shown here characterizes the distribution of pre-processed GDT scores generated by eQuant for a data set of protein structure chains with similar sequence length (± 10% relative length) to your uploaded model. Furthermore, the relation between your GDT score and the mean of pre-processed scores is expressed by a Z-score. Values significantly below the median of the box plot (respectively high Z-score) indicate for good global structure quality.

Protein Vieweri

The structure visualized by PV [Biasini, 2014].

A coloring range of 1 to 7 Å is applied: high quality scores close to 1 are depicted as blue, while regions exhibiting a high amount of local discrepancies are rendered red. Amino acids of mediocre quality are colored white.

Hover over data points in the line chart to highlight that particular amino acid. Click on it to center the view on that residue. While pressing 'Shift' you can translate the point of view. Hit 'Escape' or click the background to restore the initial view.

Local Quality Assessmenti

Analogically with the global quality score, the local quality can be quantified by the comparison with the unknown native conformation of the protein. This time though, the distance between corresponding residues is predicted.

Amino acids in the compact, hydrophobic core will likely exhibit small deviations from the native structure, whereas especially coils exposed to the solvent are prone to spatiotemporal displacement and in consequence to serious disagreements. For each amino acid of this chain the predicted distance is plotted on the y-axis. Residues with distances exceeding 3.8 Å (shaded red) indicate local discrepancies.

BioInformatics Group Mittweida (bigM), University of Applied Science Mittweida, 2018