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What is Alchemistry?
Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate the free energies of various physical processes, such as the free energy of ligand binding to a macromolecular receptor, or the transfer of a small molecule from gas to water. The alchemistry.org logo graphic above depicts such an example, where the free energy of ligand binding to a protein receptor is computed by computationally simulating alchemical intermediates with weakened interactions with the rest of the system. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant physical contributions to binding affinity.
What is here?
In these pages, we will provide information about these alchemical free energy calculations. This information falls into several categories, and some are is still to be prepared.
Things that are now here:
- Best Practices: Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work.
- Gromacs Tutorials: A set of tutorials for conducting several specific alchemical free energy calculations with the GROMACS simulation package, to allow beginners to get their feet wet.
- Free Energy References: An editable, categorized list of references with annotations relating to free energy calculations, so you can stay abreast of the latest literature, add links to your own work, and comment. The database is implemented as a CiteULike group, with over 700 articles. And probably there are another 700 that we should have up, so please join and add your favorite papers (as well as your own work!)
- Free Energy Tools: Some tools related to free energy calculations. These are evolving over time.
- Test System Repository: A repository of standard test systems (including parameters, preferably in multiple formats) for alchemical free energy calculations, along with known results with those parameters, and benchmark test sets.
Please be warned that, as this is a new page (and a Wiki), this information is in a state of flux.
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