with Kim Baldridge, Celine Amoreira, University of Zurich, and Chris Kondrick, Laura Bertsis, Celia Croy and Noah Ollikanien, San Diego Supercomputing Centre

The workflow for assessment of a protein involves selection of that protein from the Protein Data Bank, preliminary processing using PDB2PQR and/or WHATIF, generation of a ligand conformations using a tool called QMView, computation of the electrostatic field using APBS and then calculation of the binding free energy. The task of minimizing the binding energy as a function of the ligand position within the protein pocket required repeated execution of the last three of these steps.

Nimrod/O provides a flexible tool for automating this process. An evaluation may fail if the ligand is poorly placed, but by running multiple concurrent optimizations, Nimrod/O assures that some will converge to a useful result.