MediaWiki API result
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"fromtitle": "Main Page",
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"*": "<tr><td colspan=\"2\" class=\"diff-lineno\" id=\"mw-diff-left-l1\" >Line 1:</td>\n<td colspan=\"2\" class=\"diff-lineno\">Line 1:</td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\"><big>'''MediaWiki has been successfully installed.'''</big></del></div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">= Alchemistry =</ins></div></td></tr>\n<tr><td class='diff-marker'>\u00a0</td><td class='diff-context'></td><td class='diff-marker'>\u00a0</td><td class='diff-context'></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\">Consult </del>the <del class=\"diffchange diffchange-inline\">[http://meta</del>.<del class=\"diffchange diffchange-inline\">wikimedia</del>.org<del class=\"diffchange diffchange-inline\">/wiki/Help:Contents User's Guide] </del>for <del class=\"diffchange diffchange-inline\">information on using </del>the <del class=\"diffchange diffchange-inline\">wiki software</del>.</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">== What is alchemistry? ==</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">Alchemical free energy calculations employ unphysical ("alchemical") intermediates to estimate </ins>the <ins class=\"diffchange diffchange-inline\">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</ins>. <ins class=\"diffchange diffchange-inline\">The alchemistry</ins>.org <ins class=\"diffchange diffchange-inline\">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 </ins>for <ins class=\"diffchange diffchange-inline\">computing free energies, but often provides insight into </ins>the <ins class=\"diffchange diffchange-inline\">dominant physical contributions to binding affinity</ins>.</div></td></tr>\n<tr><td class='diff-marker'>\u00a0</td><td class='diff-context'></td><td class='diff-marker'>\u00a0</td><td class='diff-context'></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div>== <del class=\"diffchange diffchange-inline\">Getting started </del>==</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div>== <ins class=\"diffchange diffchange-inline\">What is here? </ins>==</div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">In these pages, we will provide information about these alchemical free energy calculations. This information falls into several categories:</ins></div></td></tr>\n<tr><td class='diff-marker'>\u00a0</td><td class='diff-context'></td><td class='diff-marker'>\u00a0</td><td class='diff-context'></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">* [[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.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">* [[Best Practices]]: Our recommendations on how alchemical free energy calculations ought to be done, with supporting literature citations and evidence from our own work.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">* [[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.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">* [[Free Energy References]]: A publicly editable, chronological list of references relating to free energy calculations, so you can stay abreast of the latest literature.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">* [[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.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">* [[Free Energy Tools]]: Some tools related to free energy calculations. These are somewhat preliminary.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">Please be warned that, as this is a new page (and a Wiki), this information is in a state of flux.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"> </ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">Ultimately, we also plan to provide a set of Python tools relating to free energy calculations here.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">== Who runs Alchemistry? ==</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">See [[About the Editors]]</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">== About the Wiki ==</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"> * Why do we need an Alchemistry wiki? [[Why Alchemistry.org?]]</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"> * HowYouCanHelp.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">== Help/Troubleshooting ==</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">Trouble viewing equations? See EquationHelp.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">== Using MediaWiki ==</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\"></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange\">* Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.</ins></div></td></tr>\n<tr><td class='diff-marker'>\u00a0</td><td class='diff-context'><div>* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]</div></td><td class='diff-marker'>\u00a0</td><td class='diff-context'><div>* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]</div></td></tr>\n<tr><td class='diff-marker'>\u00a0</td><td class='diff-context'><div>* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]</div></td><td class='diff-marker'>\u00a0</td><td class='diff-context'><div>* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]</div></td></tr>\n<tr><td class='diff-marker'>\u00a0</td><td class='diff-context'><div>* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</div></td><td class='diff-marker'>\u00a0</td><td class='diff-context'><div>* [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</div></td></tr>\n"
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