3D-PP

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Parameters

Input type

X-Ray 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.

Spacing Threshold (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.

Å

Radius Threshold (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).

Å

RMSD Threshold (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.

Å

Displacement Threshold (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.

Å

Minimum Coverage (Mc) This value allows to show only 3D-patterns with a coverage value equal to or higher than Mc.

%

Email 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