Input Type X-Ray: A text file containing the identifiers of the proteins to be processed. Download the sample file for details.

Input Type In Silico: A zip file containing the structures to be processed. Download the sample zip file for details.

Concatenate Chains: To search between chains.

Apply Fpocket: Fpocket is a protein pocket prediction algorithm. Given a PDB protein structure it enables the user to identify potent binding sites. Based on Voronoi tessellation, this algorithm is very fast and particularly well suited for large scale protein binding pocket screenings and development of scoring functions for binding pocket characterization.

Minimum Drug Score: This value is the minimum druggability score found in pockets. Druggability score intends to assess the at what point the identified pocket is likely to bind drug like molecules. This drug score is a value between 0 and 1, 0 signifying that the pocket is likely to not bind a drug like molecule and 1, that it is very likely to bind the latter.

Spacing Threshold (St): This value (in Å) 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 (Rt): This term (in Å) 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 (RMSDt): This value (in Å) is used for clustering the 3D-patterns detected and represents a measure of structural variability for the sites composing each 3D-pattern.

Displacement Threshold (Dt): This value (in Å) 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 Percentage (Mc): This value (percentage) allows to show only 3D-patterns with a coverage value equal to or higher than Mc.

Name of Job: A name to describe this job.

Email (optional): The results will be send to this email.