Welcome to Adepth

The server computes the atomic depths in proteins which is derived from trilinear interpolation of the signed distance function (SDF) at the nearest grid points surrounding the atom.

The atomic depth value is the distance of the atomic center from the solvent accessible surface.

Results are included in the PDB file in the occupancy and B-factor columns.

1. Input your PDB file
Simply enter the PDB code or upload a .pdb file.
PDB code :
 must exist in PDB 
(Type : 1AY1 as a test molecule)
or upload your PDB file :
PDB chain ID :
Probe radius :
Grid size (X, Y, Z) in Å :   
Output grid file (dx format) :
Print-out only extruded PDB :
     Min value:  Max value:
Grid boundary (in Å) :
2. Getting results
Enter a valid e-mail address where we can send a link to the results when the run is completed.
E-mail :   

If you find this site useful, please cite :
Adepth: new representation and its implications for atomic depths of macromolecules
Shu-wen W. Chen; Jean-Luc Pellequer
Nucleic Acids Research 2013

 

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