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Revision as of 15:22, 18 June 2013
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?
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.
Who runs Alchemistry?
About the Wiki
- Why do we need an Alchemistry wiki? Why Alchemistry.org?
- How You Can Help. Add your own experience to what is posted here!
Using MediaWiki in Alchemistry.org
- Creating citations on Alchemistry.org
- Wikitext markup examples
- Consult the User's Guide for information on using the wiki software.
- Configuration settings list
- MediaWiki FAQ
- MediaWiki release mailing list