pocketZebra test analysis
Read more about pre-selected datasets at the examples page
Structural data
Maximum file size: 10 MB
Allowed extensions: pdb
Maximum file size: 10 MB
Allowed extensions: pdb
This structure will be used to identify functionally important pockets and cavities.
Bioinformatic analysis
Maximum file size: 50 MB
Allowed extensions: fasta fasta_aln fa
Maximum file size: 50 MB
Allowed extensions: fasta fasta_aln fa
Multiple alignment of a protein family in fasta format that contains a sequence of the Representative PDB structure
If the Representative PDB structure contains multiple chains, select the chain that was used to build the Multiple sequence alignment
Leave the field blank to use the first chain
Maximum file size: 50 MB
Allowed extensions: fasta fasta_aln fa
Maximum file size: 50 MB
Allowed extensions: fasta fasta_aln fa
Multiple alignment of a protein family in fasta format that contains a sequence of the Representative PDB structure
If the Representative PDB structure contains multiple chains, select the chain that was used to build the Multiple sequence alignment
Leave the field blank to use the first chain
Maximum file size: 50 MB
Allowed extensions: ze
Sequence ID to be used as a reference
Default: 1 (first sequence in the alignment file)
Leave the field blank to use default value
Apply offset to the reference sequence numbering
Default: 0
Leave the field blank to use default value
Threshold amount of gaps in a column
Default: 5%
Leave the field blank to use default value
Number of random shuffles for each column
Default: 1000
Leave the field blank to use default value
Maximum file size: 10 MB
Allowed extensions: txt groupfile
Set a groupfile in txt format with definition of functional subfamilies (see explanation of Input for more details)
Amount of sequences allowed as outliers during clusterization
Default: 0.2
Example: value of '0.2' will make the program to accept classification with not more than 20% outliers compared to the sample size
Leave the field blank to use default value
Minimal number of sequences allowed in a subfamily
Default: 5% of the sample size if the field was left blank
Example: value of "3" will make the program to accept subfamilies with at least 3 sequences and larger (see explanation of Input for more details)
Leave the field blank to use default value
Minimal number of subfamilies
Default: 2
Leave the field blank to use default value
Max groups:
Maximum number of subfamilies
Default: 1000000000
Leave the field blank to use default value
Structural analysis
Maximum file size: 10 MB
Allowed extensions: txt
Minimum radius of an alpha-sphere
Default: 3.0
Leave the field blank to use default value
Maximum radius of an alpha-sphere
Default: 6.0
Leave the field blank to use default value
Minimum number of apolar neighbor
for an a-sphere to be considered as apolar
Default: 3
Leave the field blank to use default value
Minimum number of a-sphere per pocket
Default: 30
Leave the field blank to use default value
Maximum distance for first clustering algorithm
Default: 1.73
Leave the field blank to use default value
Maximum distance for single linkage clustering
Default: 2.5
Leave the field blank to use default value
Minimum number of neighbor close from
each other (not merged otherwise)
Default: 3
Leave the field blank to use default value
Maximum distance between two pockets
barycenter (merged otherwise)
Default: 4.5
Leave the field blank to use default value
Minimum proportion of apolar sphere
in a pocket (remove otherwise)
Default: 0.0
Leave the field blank to use default value
Number of Monte-Carlo iteration for the
calculation of each pocket volume
Default: 2500
Leave the field blank to use default value
Statistical analysis
Define the smallest inclusive Z-score to select subfamily-specific positions