Pose & Rank Help Page

Input Fields

• Email address: if provided, you will be notified at this email address when your job is complete (otherwise, use the link provided when you submit your job to check back for results).
• Protein coordinate file: upload file in PDB or mmCIF format.
• Ligand coordinate file: Upload file in Mol2 format.
• Score type: choose between PoseScore, for selecting near-native geometry from conformations of the same ligand (complex structure prediction) or RankScore, for selecting ligands from non-binders (virtual screening)

Output

The output of Pose & Rank is a table (score.list). Each table line contains the name of each uploaded small molecule and the corresponding PoseScore or RankScore.

Table Format:

• Ligand name: the name of the small molecule scored that should be in the next line after each "@<TRIPOS>MOLECULE" in the uploaded mol2 file.
• Score: PoseScore or RankScore [1].

References

1. Fan H, Schneidman D, Irwin JJ, Shoichet BK, Sali A. Statistical potential for modeling and ranking protein-ligand interactions. J. Chem. Inf. Model. 2011, 51:3078-92.

Offline use

To generate scores for large numbers of complexes (or for confidential structures) use the ligand_score application, part of IMP - the Integrative Modeling Platform. (This web server uses IMP internally.)