3D-PP 2.0
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Stats of jobs
Parameters
Input type X-Ray
Input type In Silico
Text file with PDB IDs (
Example
)
A text file containing the identifiers of the proteins to be processed. Download the sample file for details.
Zip file (
Example
)
A zip file containing the structures to be processed. Download the sample zip file for details.
Spacing Threshold in Å (
St
)
This value is used to create the Virtual Grid of Coordinates and defines, how broad and rigorous will be the exploration of 3D-patterns. For instance, a St = 0.5, means that every 0.5 Å in the 3D space of each protein structure, a new virtual coordinate of reference will be created.
Radius Threshold in Å (
Rt
)
This term represents the limits of the size of the 3D-patterns searched. Low Rt values are used to detect small binding sites (e.g. 3 Å), whereas high values allow to identify bigger sites (e.g. 7 Å).
RMSD Threshold in Å (
RMSDt
)
This value is used for clustering the 3D-patterns detected and represents a measure of structural variability for the sites composing each 3D-pattern.
Displacement Threshold in Å (
Dt
)
This value is used to expand the size and shape for the exploration of the 3D-patterns. By default, this value is set in 0, which means that only the spherical 3D-patterns are searched. If the user changes this value; for example, Dt=2, two new virtual centers will be considered for the searching of 3D-patterns. This option allows to obtain seven new elliptical/oval zones that will be explored to detect non spherical 3D-patterns.
Minimum Coverage % (
Mc
)
This value allows to show only 3D-patterns with a coverage value equal to or higher than Mc.
Email (optional)
The results will be send to this email.
Name of job
A name to describe this job.
School of Bioinformatics Engineering
| Department of Bioinformatics |
Universidad de Talca
| Talca, Chile