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Pose & Rank - a web server for scoring protein-ligand complexes.

Docking example

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 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)


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].


  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.)

Fan H, Schneidman-Duhovny D, Irwin J, Dong GQ, Shoichet B, Sali A. Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions. J Chem Inf Model. 2011, 51:3078-92. [ Abstract ]