Server For Computing/Predicting DEPTH, Ligand Binding Sites, pKa, Disulfide engineering


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

Parameters






Parameters



Parameters
Use Evolutionary Information







Parameters

Parameters:







Parameters with help content are in bold face. Please click on "? or the name"

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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.
  3. For Membrane PDB, we have a local database from OPM. Please check the option under Depth 'Parameters'
  4. For your own PDB with membrane, use ppm servers at OPM to get your own PDB


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.

Disulfide engineering
Grades & Angles
Grade A

1.6 ≤ rss ≤ 2.4 and 60° ≤ |𝜒ss| ≤ 120°

and

30° ≤ |𝜒i1| ≤ 90° or 150° ≤ |𝜒i1| ≤ 180°

and

30° ≤ |𝜒j1| ≤ 90° or 150° ≤ |𝜒j1| ≤ 180°

Grade B

1.6 ≤ rss ≤ 2.4 and 60° ≤ |𝜒ss| ≤ 120°

and

30° ≰ |𝜒i1| ≰ 90° or 150° ≰ |𝜒i1| ≰ 180°

and

30° ≰ |𝜒j1| ≰ 90° or 150° ≰ |𝜒j1| ≰ 180°

Grade C

1.6 ≰ rss ≰ 2.4 or 60° ≰ |𝜒ss| ≤ 120°

Grade D

Si or Sj cannot be geometrically fixed

JOBNAME
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EMAIL

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