Difference between revisions of "Main Page"

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[[Image:alchemistry.jpg|center|alchemistry logo]]
 
[[Image:alchemistry.jpg|center|alchemistry logo]]
 
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= Recent events =
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__NOTOC__
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* '''[[2010 Workshop on Free Energy Methods in Drug Design]]'''
 
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= What is Alchemistry? =
 
= What is Alchemistry? =
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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.
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Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate the free energies of various physical processes.  Such process include ligand binding to a protein receptor, the transfer of a small molecule from gas to water, or the free energy of a mutation of a side chain. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant interactions driving binding.
  
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= What is here? =
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=Getting Started with Free Energy Methods=
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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.
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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.
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<!-- This style taken from Wikipedia mainpage -->
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{| id="mp-upper" style="width: 100%; margin:4px 0 0 0; background:none; border-spacing: 0px;"
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<!--        FUNDAMENTALS AND METHODS        -->
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| class="MainPageBG" style="width:55%; border:1px solid #cef2e0; background:#f5faff; vertical-align:top; color:#000;" |
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{| id="mp-left" style="width:100%; vertical-align:top; background:#f5faff;"
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| style="padding:2px;" | <h2 id="mp-tfa-h2" style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3bfb1; text-align:left; color:#000; padding:0.2em 0.4em;">[[Free Energy Fundamentals]]</h2>
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|-
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| style="color:#000;" | <div id="mp-tfa" style="padding:2px 5px">[[file:Transformation_small.png|frameless|center]]<br/>Learn the methods and techniques behind free energy methods with in-depth coverage of free energy definitions and topics.</div>
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|-
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| style="padding:2px;" | <h2 id="mp-dyk-h2" style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3bfb1; text-align:left; color:#000; padding:0.2em 0.4em;">[[Best Practices |Best Practices in Free Energy Methods]]</h2>
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|-
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| style="color:#000; padding:2px 5px 5px;" | <div id="mp-dyk">Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work.</div>
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|-
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| style="padding:2px;" | <h2 id="mp-dyk-h2" style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3bfb1; text-align:left; color:#000; padding:0.2em 0.4em;">[http://www.citeulike.org/groupfunc/14929/home Free Energy References] </h2>
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|-
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| style="color:#000; padding:2px 5px 5px;" | <div id="mp-dyk">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 [http://www.citeulike.org/group/14929 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 (especially your own work!)
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Once you join the group, adding new articles is easy with the [http://www.citeulike.org/bookmarklets.adp | Cite-u-Like bookmarklet]
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</div>
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|-
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| style="padding:2px;" | <h2 id="mp-dyk-h2" style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3bfb1; text-align:left; color:#000; padding:0.2em 0.4em;">[[Events|Events: Conferences relating to free energy methods.]]</h2>
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|} <!---      END (LEFT) SECTION    --->
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<!--        TECHNIQUES AND EXAMPLES        -->
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| class="MainPageBG" style="width:45%; border:1px solid #cedff2; background:#f5faff; vertical-align:top;"|
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{| id="mp-right" style="width:100%; vertical-align:top; background:#f5faff;"
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| style="padding:2px;" | <h2 id="mp-itn-h2" style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">[[Example Free Energy Calculations]]</h2>
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|-
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| style="color:#000; padding:2px 5px;" | <div id="mp-itn">A look into practical examples without software-specific details. We outline the steps needed for realistic free energy problem, detailing problems you can expect to encounter, and how to analyze the data to get a robust free energy difference.</div>
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|-
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| style="padding:2px;" | <h2 id="mp-otd-h2" style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">[[Tutorials|Tutorials and How-to's]]</h2>
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|-
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| style="color:#000; padding:2px 5px 5px;" | <div id="mp-otd">[[file:ligandtranslate.png|frameless|center]]<br/>Tutorials for conducting several specific alchemical free energy calculations with a variety of simulation packages, to allow beginners to get their feet wet. These guides will walk you through setting up software-specific free energy simulations and their analysis.</div>
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|-
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| style="padding:2px;" | <h2 id="mp-otd-h2" style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">[[Test System Repository]]</h2>
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|-
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| style="color:#000; padding:2px 5px 5px;" | <div id="mp-otd">A repository of standard test systems (including parameters, often in multiple file formats) for alchemical free energy calculations, along with known results with those parameters, and benchmark test sets.</div>
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|-
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| style="padding:2px;" | <h2 id="mp-otd-h2" style="margin:3px; background:#cedff2; font-size:120%; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">[[Job postings]]</h2>
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|-
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| style="color:#000; padding:2px 5px 5px;" | <div id="mp-otd">Job postings in computational chemistry and alchemical free energy calculations.</div>
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|}
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|}
  
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Things that are now here:
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= [[Alchemistry CiteULike RSS | RSS feed of recent papers added to the Alchemistry.org database]] =
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All these papers have been linked through the [http://www.citeulike.org/group/14929 Alchemistry.org CiteULike group]. Abstracts can be accessed by the link in the section title. [http://www.citeulike.org/rss/group/14929 Get the RSS.]
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<rss max=5 template="MediaWiki:Rss-item-titleauthor">http://www.citeulike.org/rss/group/14929</rss>
  
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* [[Best Practices]]: Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work.
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= About the Alchemistry.org wiki =
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* [[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.
 
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* [http://www.alchemistry.org/references/ Free Energy References]: A publicly 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 reference database is currently being transitioned to a Zotero group, [http://www.zotero.org/groups/alchemistry web accessible here], but much more fully featured downloading the Zotero plug in.  Please contact Michael Shirts (michael.shirts at virginia.edu) for more editable access.
 
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* [[Free Energy Tools]]: Some tools related to free energy calculations. These are somewhat preliminary.
 
  
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Things that are coming:
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== Who runs Alchemistry.org? ==
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* [[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.
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* Read [[About the Editors]]
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* [[Free Energy Introduction]]: An introduction to free energy calculations generally, with a slant towards alchemical methods. Hopefully this will provide a good starting point for students beginning work in the area, and will be suitable for advanced undergraduate or early graduate students.
 
  
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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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== Contributing to Alchemistry.org ==
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* [[How You Can Help]].  Add your own experience to what is posted here!
  
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= Who runs Alchemistry? =
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== Using MediaWiki in Alchemistry.org ==
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See [[About the Editors]]
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* [[Proper_referencing|Creating citations on Alchemistry.org]]
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= About the Wiki =
 
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* Why do we need an Alchemistry wiki? [[Why Alchemistry.org?]]
 
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* [[How You Can Help]].
 
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= Using MediaWiki =
 
 
* [http://meta.wikimedia.org/wiki/Help:Wikitext_examples Wikitext markup examples]
 
* [http://meta.wikimedia.org/wiki/Help:Wikitext_examples Wikitext markup examples]
 
* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
 
* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Latest revision as of 10:37, 15 May 2016

alchemistry logo


What is Alchemistry?

Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate the free energies of various physical processes. Such process include ligand binding to a protein receptor, the transfer of a small molecule from gas to water, or the free energy of a mutation of a side chain. This approach provides not only a quantitative and rigorous method for computing free energies, but often provides insight into the dominant interactions driving binding.

Getting Started with Free Energy Methods

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.

Free Energy Fundamentals

Transformation small.png

Learn the methods and techniques behind free energy methods with in-depth coverage of free energy definitions and topics.

Best Practices in Free Energy Methods

Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work.

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 (especially your own work!)

Once you join the group, adding new articles is easy with the | Cite-u-Like bookmarklet

Events: Conferences relating to free energy methods.

Example Free Energy Calculations

A look into practical examples without software-specific details. We outline the steps needed for realistic free energy problem, detailing problems you can expect to encounter, and how to analyze the data to get a robust free energy difference.

Tutorials and How-to's

Ligandtranslate.png

Tutorials for conducting several specific alchemical free energy calculations with a variety of simulation packages, to allow beginners to get their feet wet. These guides will walk you through setting up software-specific free energy simulations and their analysis.

Test System Repository

A repository of standard test systems (including parameters, often in multiple file formats) for alchemical free energy calculations, along with known results with those parameters, and benchmark test sets.

Job postings

Job postings in computational chemistry and alchemical free energy calculations.

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. Get the RSS. Failed to load RSS feed from http://www.citeulike.org/rss/group/14929: There was a problem during the HTTP request: 403 Forbidden

About the Alchemistry.org wiki

Who runs Alchemistry.org?

Contributing to Alchemistry.org

Using MediaWiki in Alchemistry.org

Retrieved from "http://alchemistry.org/wiki/index.php?title=Main_Page&oldid=2872"