Getting Started

Getting started with DrugFinder is easy, and the Bronze service, which returns the top 100 hits, is free to academics and cancer-related projects. All you need to provide is the 3D structure of the complex of a known active ligand with its target protein. You do not need to add hydrogen atoms to the ligand and protein: just provide the coordinates of the heavy atoms.

Disclaimer

The DrugFinder service uses research software under active development. No guarantees are made regarding the accuracy of predictions. The results are provided AS IS and should be used at your own risk. We do not warrant or assume any liability or responsibility for the accuracy or usefulness of any information provided by this service.

Submission Guidelines

If you are starting with the structure of a complex, you will need to edit it and separate out the ligand from the rest of the complex.

Protein	The protein coordinates should be provided in PDB format, with the ligand removed, but other molecules (i.e. cofactors, solvent, etc.) included.
Ligand	The ligand should be provided in SDF format. Make sure that the ligand's atomic coordinates are those of the bound structure and that the atoms and bond records correctly describe the structure.
Email address	You must provide a valid email address, otherwise we will not be able to accept your submission or return your results. Requests from bulk addresses such as hotmail, yahoo and gmail will not be accepted.

Submissions will be checked for compatibility with the DrugFinder service and acknowledged. The Bronze level of service is provided free of charge to the academic research community. Requests will be queued and turnaround time will vary depending on the load on the cluster. Turnaround time for the Gold and Silver services will be agreed in advance. Commercial users wishing to use the DrugFinder service should contact drugfinder.inquiries (at) inhibox (dot) com to discuss their requirements.

You can use the free, open source program OpenBabel to convert your files into the accepted formats if they are currently in a different format; e.g., to convert the ligand from PDB format to SDF format, type the following command in a terminal at a Unix, Linux or Mac OS X prompt, to convert the ligand PDB file 'ligand.pdb' into the SDF-formatted file, 'ligand.sdf':

babel -ipdb ligand.pdb -osdf ligand.sdf

We also recommend that you use a visualization program like PyMOL to check visually that your ligand has the correct coordinated with respect to the protein, i.e. it is bound in the active site of interest.

Apply to DrugFinder