ROCS ® is a tool for aligning and scoring a database of molecules to a query or template molecule. The alignments can be used for a variety of purposes. The scores are used to rank molecules based on the probability that they share relevant (biological) properties with the query molecule.

ROCS aligns molecules based on shape similarity and their distributions of color or chemical features. The minimal inputs into ROCS are a query molecule in a single 3D conformation and a search database of molecules in multiple 3D conformations. The minimal output is a file of the best alignment and scores for each of the database molecules to the query.


The ROCS distribution comprises 2 applications:


  • Aligns and scores molecules in a database file to a query molecule.


  • A GUI application for ROCS.

  • Interactive generation, editing, and validation of queries for ROCS.

Utility Programs

The following utility programs are also included in this distribution:

  • MakeRocsDB: Generates a database in an optimized format for searching with ROCS from a database of molecules in 3D conformations from OMEGA.

  • Chunker: Divides an input database into a specified number of pieces (chunks) of similar size. Used to generate sub-databases suitable for running large calculations in a divide and conquer fashion.

  • CheckCff: Applies color features to input molecules that are set based on the input color force field file (CFF). Used to visually check that the CFF is functioning correctly.

  • HLMerge: Merges multiple output files from ROCS into single file. (Re-)ranks ROCS hits based on a specified score. Used to combine results from divide and conquer calculations on sub-databases made using chunker.

  • ROCSReport: Creates a multi-page PDF report document with the hit molecule file generated by ROCS.

Alignments from ROCS are consumed directly by EON, which calculates molecular similarity based on electrostatic potential.