Structure Code

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

DEPTH Computation
Parameters

DEPTH Solvating Cycles:
Neighbourhood Waters(1-5):
Solvent Neighbourhood Radius(Å):

ASA
Parameters

ASA Resolution:
ASA Probe Radius:

Binding Site Prediction
Parameters

Use Evolutionary Information

Blast Iterations:
Blast e_thr:
Blast maxSeq:

Solvating Cycles:
Neighbourhood Waters(1-5):
Solvent Neighbourhood Radius(Å):
Probability Threshold:

pKa Prediction
Parameters

Parameters:

Neighbourhood Waters(1-5):
Depth Solvating Cycles:
Electrostatic Distance:

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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 e_thr

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

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