Sire-Based applications

Sire has been used to create a series of task-focussed applications. Some come bundled with Sire, while others can be downloaded separately. The apps are divided into three categories; Setup, Simulation and Analysis.

If you have developed a Sire app and want to include it in this list, please get in touch.

Setup Apps

• FESetup : App developed with CCP-Biosim, used to set up binding free energy calculations.
• align : Bundled app used to align molecules on top of each other.
• transform : Bundled app used to translate and rotate molecules.

Simulation Apps

• waterswap : Bundled app used to calculate absolute binding free energies.
• ligandswap : Bundled app used to calculate relative binding free energies.
• quantomm : Bundled app used to calculate differences in free energy between quantum mechanics (QM) and molecular mechanics (MM) representations of a molecule. Used to “correct” molecular mechanics free energies to QM or QM/MM.

Analysis Apps

• analyse_freenrg : Bundled app used to generate potentials of mean force (PMFs) and calculate total free energies from the average energy components output by Sire free energy apps (e.g. waterswap, ligandswap and quantomm).
• waterview : Bundled app used to generate and view average water populations in protein-ligand binding sites.