Server For Computing/Predicting DEPTH, Cavity Sizes, Ligand Binding Sites and pKa


Four letter PDB complex code or upload file in PDB format.

Parameters






Parameters
Use Evolutionary Information








Parameters

Parameters:




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PDB Structure

The PDB structure is the primary input to the server. The PDB structure can be specified in the following ways:

1. By writing the four letter valid PDB complex code
2. By uploading a valid PDB file.

Caution: If a wrong PDB code is entered or if the uploaded file is not a valid PDB file then the job will be rejected by the server and the user will be informed of the respective error.

Number of DEPTH cycles

The number of cycle to run depth, default is 25.

Number of Neighbour water molecules

The number of neighbor water in depth calculation, default is 2.

Solvent Neighbourhood Radius(Å)

Solvent Radius, default is 4.2

ASA Resolution

The resolution for solvent accessible surface area calculation, default is 92.

Cutoff distance for Electrostatic calculation

Probe radius for solvent accessible surface area calculation, default is 1.4.

Evolutionary Information

Uses Blast

Blast Iterations

Blast Iterations

Blast e_thr

Blast e_thr

Blast maxSeq

Blast maxSeq

Neibourhood Waters

Neighbourhood waters

Probability Threshold

Prob Threshold

Number of DEPTH cycles

The number of cycle to run depth, default is 25.

Number of Neighbour water molecules

The number of neighbor water in depth calculation, default is 2.

Solvent Neighbourhood Radius(Å)

Solvent Radius, default is 4.2

Cutoff distance for Electrostatic calculation

The cut-off distance for electrostatic calculation, default is 12.

JOBNAME
The jobname is chosen by the user for the job. Jobname is useful when the user wants to distinguish between the different submitted job(s).
EMAIL

If the user provide an email address then an email notification will be sent to inform the user about the job completion or unexpected termination of the job.

It is advised that a valid and active email address must be provided to receive notifications about the job status.