ChExVis

PDB-ID:

PDB id of protein structure available on RCSB database.

Or, Upload PDB file:

Upload PDB file in text format.

Alpha:

Controls the size of atoms at which cavities are computed. Alpha=0 corresponds to no change in radius while higher values mean radii are increased.

Probe Radius (Å):

Radius of the probe molecule. By default 1.00Å is taken as probe radius. If you don't get expected results, try reducing this value. You can even set it to 0Å to consider channel of any width as feasible.

Compute channels to active sites

For active site identification: Use CSA database.

Use HETATM records.

User Defined.

User defined sites:

Enter residue IDs of active sites separated by space. Mutiple active sites should be separated by commas. e.g. LEU:A:17 VAL:A:22, PRO:A:41

Start point approximation: Centroid Deepest point in the vicinity

Compute Pores

Auto end points:

Number of end points to automatically select for pore computation.

Compute Trans-membrane Pores

Inside points:

Number of end points to select inside the cell.

Outside points:

Number of end points to select outside the cell.

Trans-membrane Classification: OPM TMHMM

Also compute widest channels.

Compute Widest Path Tree.

Compute electro-static potential profile.

APBS field for the molecule is computed and then it is mapped onto the channels. Note: Time consuming.

Compute conservation profile.

Compute conservation profile for the channels based on conservation of residues. Note: Time consuming.

Email:

Send the result link to this Email ID when the job is finished.

ChExVis Job Form

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