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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 graphic above depicts such an example, where the free energy of ligand binding to a protein receptor is computed by 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?
This site is designed to both give novices best practices information about how to perform free energy calculations, and to provide an ongoing reference for the current state of research into methods for calculating free energies.
- Best Practices: Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work.
- Tutorials: Tutorials for conducting several specific alchemical free energy calculations with a variety of simulation packages, to allow beginners to get their feet wet.
- Free Energy Fundamentals: In-depth coverage of free energy definitions and topics. More complete than the Best Practices Section
- 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!)
- 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.
- Events: Conferences relating to free energy methods
Please be warned that, as this is a new page (and a Wiki), this information is in a state of flux.
RSS feed of recent papers added to the Alchemistry.org database
All these papers have been linked through the Alchemistry.org CiteULike group. Abstracts can be accessed by the link in the section title. Failed to load RSS feed from http://www.citeulike.org/rss/group/14929: There was a problem during the HTTP request: 403 Forbidden
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