LIGSITE^csc is a web server for the automatic identification of pockets on protein surface using the Connolly surface and the degree of conservation!

Input methods:

Help

1. A user may upload his/her own pdbfile
   
2. A user may enter a PDB code and chain ID
   
3. A user may adjust the parameters
   

Upload a PDB file

Help

      PDB file :

Or enter a PDB ID:

Help

      PDB ID:  (For example 1acb)
      Chain ID:     (For example E, I)
      ( If no chain ID is given, the whole structure is considered. Separate multiple chain IDs by commas.)
      Re-rank by conservation

Set up the parameters:

Help

      Please choose the grid space:
      1.0 1.5 2.0 Angstrom.
      How many pockets do you want?      
      Radius of the probe to get potential binding sites:
      Angstrom.

  

Note:
It will take up to 30 seconds to find pockets depending on the size of your protein and the parameters you set. Please be patient.
The algorithm of LIGSITE^csc is illustrated here.

We have developed a new web-server called metaPocket. Please visit it for more accurate ligand binding site prediction.

Download:

Want to run LIGSITE^csc locally? Get the source code here.

Reference:

If you find this server useful for your work, please cite: Bingding Huang and Michael Schroeder (2006), LIGSITE^csc: predicting protein binding sites using the Connolly surface and degree of conservation, BMC structural Biology, 6:19. ( link pdf )

Contact:

Bingding Huang, e-mail: bhuang@biotec.tu-dresden.de, homepage.

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Last update: 10th, June, 2007

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Bioinformatics group                     Biotec                                 TU Dresden