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LigSearch Identification of possible ligands from 3D protein structure or sequence

The aim of the LigSearch server is to help identify ligands that bind to a protein. It utilizes resources such as ChEMBL, ChEBI and various other servers to find potential ligands. From this page you can submit your own structure, sequence or UniProt code to find potential ligands. When the results are done you will receive an email. You can also retrieve the results of a previously submitted run. LigSearch

Choose option A, B, C, D or E:

A. Upload PDB-format file:
 
B. Use existing PDB file (4 chars):  
Runs LigSearch on an existing PDB entry or, if already done, takes you directly to the results page.
 
C.  UniProt Accession Code:
   
D. Pasted sequence:
Enter a sequence of single-letter amino acid codes. Blank spaces will be ignored.
 
E. Go to previous analysis   Id no.:   Security code:

Notes

- Please try to limit the number of structures/sequences submitted to about 5 per hour to avoid overloading the server. To arrange a large batch run, please contact us.
- Some of the methods take minutes to run; others take hours. You will be notified by e-mail when the entire process is complete.
- The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.
- If your structure contains any non-standard amino acids (eg selenomethionines, phosphotyrosines, etc.) it is a good idea to rename them in your PDB file to their closest standard equivalents. This will increase the chances of LigSearch finding matches to both sequence and structure templates. (For selenomethionines identified by residue name MSE there is no need to make any changes).
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Related databases

PDBsum
Structural analyses of all PDB entries

ProFunc
Prediction of protein function from 3D structure