Difference between revisions of "Main Page"

From AlchemistryWiki

Latest revision as of 10:37, 15 May 2016

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

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

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?

Read About the Editors

Contributing to 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.
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-= Alchemistry.org is locked while we update =
-We are in the process of updating the MediaWiki version! We have locked the wiki so no edits can be made until we ensure everything is working.
-During this time, some pages, math, and images may not display correctly. We apologize for any inconvenience this may cause.
-If you have questions or concerns, please feel free to contact Levi Naden at lnaden@virginia.edu.
 = 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.
+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.
-= What is here? =
+=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.
+<!-- This style taken from Wikipedia mainpage -->
+{| id="mp-upper" style="width: 100%; margin:4px 0 0 0; background:none; border-spacing: 0px;"
+<!--        FUNDAMENTALS AND METHODS        -->
+| class="MainPageBG" style="width:55%; border:1px solid #cef2e0; background:#f5faff; vertical-align:top; color:#000;" |
+{| id="mp-left" style="width:100%; vertical-align:top; background:#f5faff;"
+| 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>
+|-
+| 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>
+|-
+| 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>
+|-
+| 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>
+|-
+| 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>
+|-
+| 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!)
+Once you join the group, adding new articles is easy with the [http://www.citeulike.org/bookmarklets.adp | Cite-u-Like bookmarklet]
+</div>
+|-
+| 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>
+|-
+|} <!---      END (LEFT) SECTION     --->
+| style="border:1px solid transparent;" |
+<!--        TECHNIQUES AND EXAMPLES        -->
+| class="MainPageBG" style="width:45%; border:1px solid #cedff2; background:#f5faff; vertical-align:top;"|
+{| id="mp-right" style="width:100%; vertical-align:top; background:#f5faff;"
+| 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>
+|-
+| 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>
+|-
+| 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>
+|-
+| 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>
+|-
+| 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>
+|-
+| 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>
+|-
+| 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>
+|-
+| style="color:#000; padding:2px 5px 5px;" | <div id="mp-otd">Job postings in computational chemistry and alchemical free energy calculations.</div>
+|}
+|}
-* [[Best Practices]]: Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work.
+= [[Alchemistry CiteULike RSS | RSS feed of recent papers added to the Alchemistry.org database]] =
-* [[Tutorials]]: Tutorials for conducting several specific alchemical free energy calculations with a variety of simulation packages, to allow beginners to get their feet wet.
+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.]
-* [[Free Energy Fundamentals]]: In-depth coverage of free energy definitions and topics.  More complete than the [[Best Practices]] Section
+<rss max=5 template="MediaWiki:Rss-item-titleauthor">http://www.citeulike.org/rss/group/14929</rss>
-* [http://www.citeulike.org/groupfunc/14929/home 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.
+= About the Alchemistry.org wiki =
-= Who runs Alchemistry? =
+== Who runs Alchemistry.org? ==
-See [[About the Editors]]
+* Read [[About the Editors]]
-= About the Wiki =
+== Contributing to Alchemistry.org ==
-* 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 =
+== Using MediaWiki in Alchemistry.org ==
 * [[Proper_referencing|Creating citations on Alchemistry.org]]
 * [http://meta.wikimedia.org/wiki/Help:Wikitext_examples Wikitext markup examples]