diff --git a/index.xml b/index.xml
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@@ -35,7 +35,8 @@ Bannan’s Abstract: The Open Force Field Initiative is developing a mac
 Modeling tools based on force fields assist development of therapies for diseases such as cancer and neurodegenerative disease throughout academia and industry.</description></item><item><title>Support for open source cheminformatics toolkits is coming!</title><link>https://asapdiscovery.org/news/rdkit-support-is-coming/</link><pubDate>Sun, 30 Sep 2018 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/news/rdkit-support-is-coming/</guid><description>We&amp;rsquo;ve been hard at work with a large-scale infrastructure overhaul of our main openforcefield toolkit following the Open Force Field Toolkit 0.1.0 prerelease, which provided an initial reference implementation of the SMIRNOFF 0.1 specification for direct chemical perception. Many thanks to all the users who provided helpful feedback in how we could improve overall usability!
 While we expect the updated toolkit to be released very soon, we wanted to provide a summary of the coming changes to give you an idea of what we&amp;rsquo;ve been up to:</description></item><item><title>Introducing the Open Force Field Initiative</title><link>https://asapdiscovery.org/news/introducing-the-initiative/</link><pubDate>Fri, 21 Sep 2018 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/news/introducing-the-initiative/</guid><description>Molecular modeling is widely used in diverse pharmaceutical discovery applications, but its utility and predictive power is limited by the accuracy of the underlying molecular mechanics force field used to compute the energetics of biomolecular systems. The Open Force Field Initiative is an open effort to build iteratively more accurate force fields to improve predictive design, along with the necessary infrastructure to make these force fields easier to build and use, and to provide a modern platform for powering force field science.</description></item><item><title>Viral Families</title><link>https://asapdiscovery.org/outputs/viral-families/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/viral-families/</guid><description>ASAP aims to discover direct-acting antivirals with broad antiviral activity within a viral family, but the difficulty of achieving this goal means that some of our program objectives are more narrowly focused on viral family members of greatest pandemic concern.
 coronaviridae Coronavirus antiviral discovery is funded by NIAID grant U19AI171399 from the National Institutes of Health.
-flaviviridae Flavivirus antiviral discovery is funded by NIAID grant U19AI171399 from the National Institutes of Health.</description></item><item><title>Targeting Opportunities</title><link>https://asapdiscovery.org/outputs/targeting-opportunities/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/targeting-opportunities/</guid><description>A targeting opportunity provides an overview of the opportunity for targeting new antivirals to a specific target protein and mode of action. This overview is intended to summarize relevant information for drug hunters, including the relevant domain and binding sites to target, notable chemical matter, rationale for antiviral effects, and other useful information in prosecuting a discovery compaign aginst the target.
+flaviviridae Flavivirus antiviral discovery is funded by NIAID grant U19AI171399 from the National Institutes of Health.</description></item><item><title>Software</title><link>https://asapdiscovery.org/outputs/software/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/software/</guid><description>Software produced by ASAP.
+argos [GitHub] A web-based visualization tool for viewing DMS data on protein structures that allows users to generate and share these views using a web UI. See &amp;lsquo;choppa&amp;rsquo; package below. Contributing Projects and Cores: Project 2 Computational Chemistry Core asapdiscovery [GitHub] [Documentation] Monorepository for running computational chemistry project support for ASAP&amp;rsquo;s viral targets, including docking, free energy calculations, chemoinformatics and machine learning. Contributing Projects and Cores: Project 5 Computational Chemistry Core choppa [GitHub] [Documentation] A Python library for visualizing Deep Mutational Scanning data and other fitness data directly onto protein structures to enable fitness-informed decision-making in medicinal chemistry workflows in P2-P5 of ASAP&amp;rsquo;s drug discovery pipeline.</description></item><item><title>Targeting Opportunities</title><link>https://asapdiscovery.org/outputs/targeting-opportunities/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/targeting-opportunities/</guid><description>A targeting opportunity provides an overview of the opportunity for targeting new antivirals to a specific target protein and mode of action. This overview is intended to summarize relevant information for drug hunters, including the relevant domain and binding sites to target, notable chemical matter, rationale for antiviral effects, and other useful information in prosecuting a discovery compaign aginst the target.
 Targeting Opportunity: SARS-CoV-2 / MERS-CoV Mpro protease [Targeting Opportunity] Contributing Projects and Cores: Project 1 Project 5 [2023-03-19] Initial draft [2024-04-29] Major update of the targeting opportunity covering clinical background, history of outbreaks, viral biology, target biochemistry, phylogenetic analysis, etc.</description></item><item><title>Molecules</title><link>https://asapdiscovery.org/outputs/molecules/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/molecules/</guid><description>SARS-CoV-2/MERS-CoV Mpro lead optimization assay data [metadata] [(negative) biochemical and liver microsome assay data [Oct 2023]] [(negative) biochemical and liver microsome assay data [Mar 2024]] [SARS-CoV-2 Mpro assay protocol] [MERS-CoV Mpro assay protocol] This data release contains assay data for compounds ASAP is not pursuing toward nomination of a development candidate as part of this discovery program. Contributing Projects and Cores: Project 5 Biochemical Assay Core Data Core [2023-04-30] Initial public release of negative biochemical activity data for 182 molecules.</description></item><item><title>Structures</title><link>https://asapdiscovery.org/outputs/structures/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/structures/</guid><description>MERS-CoV/SARS-CoV-2 Mpro protease ASAP-COV-MPRO XChem crystallographic fragment screen of SARS-CoV-2 Mpro xray-fragment-screen [ 2020-03-18 ] Contributing Projects and Cores: Project 2 Structural Biology Core We performed an exhaustive crystallographic fragment screen to probe the Mpro active site, and to identify opportunities for fragment merging or growing. Additionally, a library of mild electrophilic fragments was screened by mass spectrometry for probing the binding properties around the active site cysteine. Overall, a total of 1742 soaking and 1139 co-crystallization experiments resulted in 1877 mounted crystals.</description></item><item><title>Publications</title><link>https://asapdiscovery.org/outputs/publications/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/publications/</guid><description>ASAP aims to publish preprints to ensure our scientific advances are rapidly and openly available.</description></item><item><title>Analysis of Circulating Variants</title><link>https://asapdiscovery.org/outputs/circulating-variants/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/circulating-variants/</guid><description>Analysis of circulating variants of SARS-CoV-2 nsp5 Mpro protease [interactive viewer] [bioRxiv preprint] Interactive viewer and dataset download of functional mutation impact scores derived from analysis of circulating SARS-CoV-2 variants Contributing Projects and Cores: Project 1 [2023-01-31] Preprint and interactive mutation viewer posted. Analysis of circulating variants of SARS-CoV-2 nsp15 endoribonuclease [interactive viewer] [bioRxiv preprint] Interactive viewer and dataset download of functional mutation impact scores derived from analysis of circulating SARS-CoV-2 variants Contributing Projects and Cores: Project 1 [2023-01-31] Preprint and interactive mutation viewer posted.</description></item><item><title>Target Product Profiles (TPPs)</title><link>https://asapdiscovery.org/outputs/target-product-profiles/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/target-product-profiles/</guid><description>A Target Product Profile (TPP) describes the desired characteristics of a drug product aimed to treat a particular disease or set of diseases.
 All ASAP TPPs are draft TPPs intended to help guide the development of target candidate profiles (TCPs) for antiviral discovery within the ASAP Discovery Consortium. ASAP works with stakeholders around the globe (such as the World Health Organization) to align TPPs to ensure they meet the needs of communities and fulfill our mission of global, equitable, and affordable access to antiviral therapies.</description></item><item><title>Target Enabling Packages (TEPs)</title><link>https://asapdiscovery.org/outputs/target-enabling-packages/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/target-enabling-packages/</guid><description>A Target Enabling Package (TEP) is a complete data package needed to enable structure-based drug discovery against an antiviral target. Pioneered by the Structural Genomics Consortium, each TEP contains relevant protein constructs and plasmid resources for one or more viral family members, protein expression and purification protocols, crystallization conditions, structures from an X-ray fragment screen at the Diamond Light Source XChem facility, small molecule hits, and biochemical assay protocols with at least one validated inhibitor with quantifiable activity.</description></item><item><title>Assay Cascades</title><link>https://asapdiscovery.org/outputs/assay-cascades/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/assay-cascades/</guid><description>An assay cascade is a defined set of assays and progression criteria used by a drug discovery program to achieve its Target Candidate Profile (TCP) goals in a time- and cost-effective manner.
 Assay cascade for MERS-CoV / SARS-CoV-2 oral antiviral [Asay Cascade (lead optimization)] Contributing Projects and Cores: Project 5 Biochemical Assay Core Structural Biology Core Antiviral Core [2022-06-01] Initial draft DENV/ZIKV NS2B/3 3C protease [Assay Cascade] Assay cascade for DENV/ZIKV NS2B/3 3C Protease oral antiviral Contributing Projects and Cores: Project 3 Project 5 Biochemical Assay Core Structural Biology Core Antiviral Core [2023-12-23] Initial draft EV-D68 / EV-A71 3C Protease Assay Cascade [Assay Cascade] Assay cascade for EV-D68 / EV-A71 3C Protease oral antiviral Contributing Projects and Cores: Project 3 Project 5 Biochemical Assay Core Structural Biology Core Antiviral Core [2022-07-14] Initial draft Assay cascade for SARS-CoV-2 nsp3 Mac1 macrodomain oral antiviral [Assay Cascade (fragment-to-lead)] Partial SARS-CoV-2 nsp3 Mac1 macrodomain assay cascade for lead nomination Contributing Projects and Cores: Project 3 Project 5 Biochemical Assay Core Structural Biology Core Antiviral Core [2022-06-01] Initial draft Assay cascade for SARS-CoV-2 Mpro oral antiviral [Assay Cascade (lead optimization)] Assay cascade for lead optimization campaign for SARS-CoV-2 noncovalent oral inhibitor from the COVID Moonshot [2020-03-23] Initial draft for COVID Moonshot</description></item><item><title>Assay Protocols</title><link>https://asapdiscovery.org/outputs/assay-protocols/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/assay-protocols/</guid><description>ASAP frequently needs to develop or scale its own biochemical assay protocols to drive discovery programs. Whenever possible, we share these protocols through protocols.io, an industry standard platform for sharing and annotating assay protocols.
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href=https://www.choderalab.org/news/2021/10/26/asap-avidd-proposal>Concept</a></li><li><a href=/members/>Members</a></li><li><a href=/sab/>SAB</a></li><li><a href=/faq/>FAQ</a></li><li><a href=/awards/>Awards</a></li><li><a href=/forum/>Open Science Forum</a></li><li><a href=https://postera.ai/moonshot/>COVID Moonshot</a></li></ul></nav><nav id=top-nav-extra><ul></ul></nav></div></header><main><div id=main><div id=hero><h1>ASAP Discovery Outputs</h1></div><div id=components><div class="row gutters"><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/viral-families/>Viral Families</a></h4><p>Viral families targeted by ASAP</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/targeting-opportunities/>Targeting Opportunities</a></h4><p>ASAP identified discovery opportunities for broad antiviral activity</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/molecules/>Molecules</a></h4><p>Assayed compounds and biochemical data</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/structures/>Structures</a></h4><p>Structures of ASAP targets with inhibitors</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/publications/>Publications</a></h4><p>Scientific publications from ASAP</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/circulating-variants/>Analysis of Circulating Variants</a></h4><p>Analysis of circulating variants to identify potential resistance liabilities in functionally tolerated mutations</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/target-product-profiles/>Target Product Profiles (TPPs)</a></h4><p>Target Product Profiles (TPPs) guiding ASAP discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/target-enabling-packages/>Target Enabling Packages (TEPs)</a></h4><p>ASAP Target Enabling Packages (TEPs) for initiating structure-based drug discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/assay-cascades/>Assay Cascades</a></h4><p>Assay cascades used by ASAP Discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/assay-protocols/>Assay Protocols</a></h4><p>Assay protocols developed for ASAP Discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/target-candidate-profiles/>Target Candidate Profiles (TCPs)</a></h4><p>Target Candidate Profiles (TCPs) guiding ASAP discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/preclinical/>Preclinical programs</a></h4><p>Preclinical data packages</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/investigational-new-drugs/>Investigational New Drug (IND) filings</a></h4><p>IND (and IND-equivalent) filing packages for ASAP preclinical programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/clinical-trials/>Clinical trials</a></h4><p>ASAP clinical trials</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/new-drug-approvals/>New Drug Approvals</a></h4><p>ASAP New Drug Approvals (NDAs)</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/img/icons/readme/></a></h4><p></p></div></div></div></div></main><footer><footer id=footer><nav><ul><li><span>ASAP Discovery</span></li><li><a href=/concept>About Us</a></li><li><a href=/credits>Image Credits</a></li><li><a href=mailto:maggie.jameson@choderalab.org>Contact Us</a></li></ul></nav></footer><link rel=stylesheet href=https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.7.1/katex.min.css integrity=sha384-wITovz90syo1dJWVh32uuETPVEtGigN07tkttEqPv+uR2SE/mbQcG7ATL28aI9H0 crossorigin=anonymous><script src=https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.7.1/katex.min.js 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href=/css/font.css rel=stylesheet type=text/css><link href=/css/kube.css rel=stylesheet type=text/css><link href=/css/kube.legenda.css rel=stylesheet type=text/css><link href=/css/highlight.css rel=stylesheet type=text/css><link href=/css/master.css rel=stylesheet type=text/css><link href=/css/kube.demo.css rel=stylesheet type=text/css><link href=/css/custom.css rel=stylesheet type=text/css><script src=/js/jquery-2.1.4.min.js type=text/javascript></script><script type=text/javascript src=/js/tocbot.min.js></script></head><body class=page-kube><header><div class=show-sm><div id=nav-toggle-box><div id=nav-toggle-brand><a href=/>ASAP Discovery Consortium</a></div><a data-component=toggleme data-target=#top href=# id=nav-toggle><i class=kube-menu></i></a></div></div><div class=hide-sm id=top><div id=top-brand><a href=/ title=home>ASAP Discovery Consortium</a></div><nav id=top-nav-main><ul><li><a href=/pipeline/>Pipeline</a></li><li><a href=/outputs/>Outputs</a></li><li><a href=https://www.choderalab.org/news/2021/10/26/asap-avidd-proposal>Concept</a></li><li><a href=/members/>Members</a></li><li><a href=/sab/>SAB</a></li><li><a href=/faq/>FAQ</a></li><li><a href=/awards/>Awards</a></li><li><a href=/forum/>Open Science Forum</a></li><li><a href=https://postera.ai/moonshot/>COVID Moonshot</a></li></ul></nav><nav id=top-nav-extra><ul></ul></nav></div></header><main><div id=main><div id=hero><h1>ASAP Discovery Outputs</h1></div><div id=components><div class="row gutters"><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/viral-families/>Viral Families</a></h4><p>Viral families targeted by ASAP</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/software/>Software</a></h4><p>Software produced by ASAP</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/targeting-opportunities/>Targeting Opportunities</a></h4><p>ASAP identified discovery opportunities for broad antiviral activity</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/molecules/>Molecules</a></h4><p>Assayed compounds and biochemical data</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/structures/>Structures</a></h4><p>Structures of ASAP targets with inhibitors</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/publications/>Publications</a></h4><p>Scientific publications from ASAP</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/circulating-variants/>Analysis of Circulating Variants</a></h4><p>Analysis of circulating variants to identify potential resistance liabilities in functionally tolerated mutations</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/target-product-profiles/>Target Product Profiles (TPPs)</a></h4><p>Target Product Profiles (TPPs) guiding ASAP discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/target-enabling-packages/>Target Enabling Packages (TEPs)</a></h4><p>ASAP Target Enabling Packages (TEPs) for initiating structure-based drug discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/assay-cascades/>Assay Cascades</a></h4><p>Assay cascades used by ASAP Discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/assay-protocols/>Assay Protocols</a></h4><p>Assay protocols developed for ASAP Discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/target-candidate-profiles/>Target Candidate Profiles (TCPs)</a></h4><p>Target Candidate Profiles (TCPs) guiding ASAP discovery programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/preclinical/>Preclinical programs</a></h4><p>Preclinical data packages</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/investigational-new-drugs/>Investigational New Drug (IND) filings</a></h4><p>IND (and IND-equivalent) filing packages for ASAP preclinical programs</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/clinical-trials/>Clinical trials</a></h4><p>ASAP clinical trials</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/new-drug-approvals/>New Drug Approvals</a></h4><p>ASAP New Drug Approvals (NDAs)</p></div><div class="col col-4 item"><h4><a href=https://asapdiscovery.org/outputs/img/icons/readme/></a></h4><p></p></div></div></div></div></main><footer><footer id=footer><nav><ul><li><span>ASAP Discovery</span></li><li><a href=/concept>About Us</a></li><li><a href=/credits>Image Credits</a></li><li><a href=mailto:maggie.jameson@choderalab.org>Contact Us</a></li></ul></nav></footer><link rel=stylesheet href=https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.7.1/katex.min.css 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diff --git a/outputs/index.xml b/outputs/index.xml
index fdc56f04..1b117f32 100644
--- a/outputs/index.xml
+++ b/outputs/index.xml
@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="utf-8" standalone="yes"?><rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom"><channel><title>ASAP Discovery Outputs on ASAP Discovery Consortium</title><link>https://asapdiscovery.org/outputs/</link><description>Recent content in ASAP Discovery Outputs on ASAP Discovery Consortium</description><generator>Hugo</generator><language>en-us</language><atom:link href="https://asapdiscovery.org/outputs/index.xml" rel="self" type="application/rss+xml"/><item><title>Viral Families</title><link>https://asapdiscovery.org/outputs/viral-families/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/viral-families/</guid><description>ASAP aims to discover direct-acting antivirals with broad antiviral activity within a viral family, but the difficulty of achieving this goal means that some of our program objectives are more narrowly focused on viral family members of greatest pandemic concern.
 coronaviridae Coronavirus antiviral discovery is funded by NIAID grant U19AI171399 from the National Institutes of Health.
-flaviviridae Flavivirus antiviral discovery is funded by NIAID grant U19AI171399 from the National Institutes of Health.</description></item><item><title>Targeting Opportunities</title><link>https://asapdiscovery.org/outputs/targeting-opportunities/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/targeting-opportunities/</guid><description>A targeting opportunity provides an overview of the opportunity for targeting new antivirals to a specific target protein and mode of action. This overview is intended to summarize relevant information for drug hunters, including the relevant domain and binding sites to target, notable chemical matter, rationale for antiviral effects, and other useful information in prosecuting a discovery compaign aginst the target.
+flaviviridae Flavivirus antiviral discovery is funded by NIAID grant U19AI171399 from the National Institutes of Health.</description></item><item><title>Software</title><link>https://asapdiscovery.org/outputs/software/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/software/</guid><description>Software produced by ASAP.
+argos [GitHub] A web-based visualization tool for viewing DMS data on protein structures that allows users to generate and share these views using a web UI. See &amp;lsquo;choppa&amp;rsquo; package below. Contributing Projects and Cores: Project 2 Computational Chemistry Core asapdiscovery [GitHub] [Documentation] Monorepository for running computational chemistry project support for ASAP&amp;rsquo;s viral targets, including docking, free energy calculations, chemoinformatics and machine learning. Contributing Projects and Cores: Project 5 Computational Chemistry Core choppa [GitHub] [Documentation] A Python library for visualizing Deep Mutational Scanning data and other fitness data directly onto protein structures to enable fitness-informed decision-making in medicinal chemistry workflows in P2-P5 of ASAP&amp;rsquo;s drug discovery pipeline.</description></item><item><title>Targeting Opportunities</title><link>https://asapdiscovery.org/outputs/targeting-opportunities/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/targeting-opportunities/</guid><description>A targeting opportunity provides an overview of the opportunity for targeting new antivirals to a specific target protein and mode of action. This overview is intended to summarize relevant information for drug hunters, including the relevant domain and binding sites to target, notable chemical matter, rationale for antiviral effects, and other useful information in prosecuting a discovery compaign aginst the target.
 Targeting Opportunity: SARS-CoV-2 / MERS-CoV Mpro protease [Targeting Opportunity] Contributing Projects and Cores: Project 1 Project 5 [2023-03-19] Initial draft [2024-04-29] Major update of the targeting opportunity covering clinical background, history of outbreaks, viral biology, target biochemistry, phylogenetic analysis, etc.</description></item><item><title>Molecules</title><link>https://asapdiscovery.org/outputs/molecules/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/molecules/</guid><description>SARS-CoV-2/MERS-CoV Mpro lead optimization assay data [metadata] [(negative) biochemical and liver microsome assay data [Oct 2023]] [(negative) biochemical and liver microsome assay data [Mar 2024]] [SARS-CoV-2 Mpro assay protocol] [MERS-CoV Mpro assay protocol] This data release contains assay data for compounds ASAP is not pursuing toward nomination of a development candidate as part of this discovery program. Contributing Projects and Cores: Project 5 Biochemical Assay Core Data Core [2023-04-30] Initial public release of negative biochemical activity data for 182 molecules.</description></item><item><title>Structures</title><link>https://asapdiscovery.org/outputs/structures/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/structures/</guid><description>MERS-CoV/SARS-CoV-2 Mpro protease ASAP-COV-MPRO XChem crystallographic fragment screen of SARS-CoV-2 Mpro xray-fragment-screen [ 2020-03-18 ] Contributing Projects and Cores: Project 2 Structural Biology Core We performed an exhaustive crystallographic fragment screen to probe the Mpro active site, and to identify opportunities for fragment merging or growing. Additionally, a library of mild electrophilic fragments was screened by mass spectrometry for probing the binding properties around the active site cysteine. Overall, a total of 1742 soaking and 1139 co-crystallization experiments resulted in 1877 mounted crystals.</description></item><item><title>Publications</title><link>https://asapdiscovery.org/outputs/publications/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/publications/</guid><description>ASAP aims to publish preprints to ensure our scientific advances are rapidly and openly available.</description></item><item><title>Analysis of Circulating Variants</title><link>https://asapdiscovery.org/outputs/circulating-variants/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/circulating-variants/</guid><description>Analysis of circulating variants of SARS-CoV-2 nsp5 Mpro protease [interactive viewer] [bioRxiv preprint] Interactive viewer and dataset download of functional mutation impact scores derived from analysis of circulating SARS-CoV-2 variants Contributing Projects and Cores: Project 1 [2023-01-31] Preprint and interactive mutation viewer posted. Analysis of circulating variants of SARS-CoV-2 nsp15 endoribonuclease [interactive viewer] [bioRxiv preprint] Interactive viewer and dataset download of functional mutation impact scores derived from analysis of circulating SARS-CoV-2 variants Contributing Projects and Cores: Project 1 [2023-01-31] Preprint and interactive mutation viewer posted.</description></item><item><title>Target Product Profiles (TPPs)</title><link>https://asapdiscovery.org/outputs/target-product-profiles/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/target-product-profiles/</guid><description>A Target Product Profile (TPP) describes the desired characteristics of a drug product aimed to treat a particular disease or set of diseases.
 All ASAP TPPs are draft TPPs intended to help guide the development of target candidate profiles (TCPs) for antiviral discovery within the ASAP Discovery Consortium. ASAP works with stakeholders around the globe (such as the World Health Organization) to align TPPs to ensure they meet the needs of communities and fulfill our mission of global, equitable, and affordable access to antiviral therapies.</description></item><item><title>Target Enabling Packages (TEPs)</title><link>https://asapdiscovery.org/outputs/target-enabling-packages/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/target-enabling-packages/</guid><description>A Target Enabling Package (TEP) is a complete data package needed to enable structure-based drug discovery against an antiviral target. Pioneered by the Structural Genomics Consortium, each TEP contains relevant protein constructs and plasmid resources for one or more viral family members, protein expression and purification protocols, crystallization conditions, structures from an X-ray fragment screen at the Diamond Light Source XChem facility, small molecule hits, and biochemical assay protocols with at least one validated inhibitor with quantifiable activity.</description></item><item><title>Assay Cascades</title><link>https://asapdiscovery.org/outputs/assay-cascades/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/assay-cascades/</guid><description>An assay cascade is a defined set of assays and progression criteria used by a drug discovery program to achieve its Target Candidate Profile (TCP) goals in a time- and cost-effective manner.
 Assay cascade for MERS-CoV / SARS-CoV-2 oral antiviral [Asay Cascade (lead optimization)] Contributing Projects and Cores: Project 5 Biochemical Assay Core Structural Biology Core Antiviral Core [2022-06-01] Initial draft DENV/ZIKV NS2B/3 3C protease [Assay Cascade] Assay cascade for DENV/ZIKV NS2B/3 3C Protease oral antiviral Contributing Projects and Cores: Project 3 Project 5 Biochemical Assay Core Structural Biology Core Antiviral Core [2023-12-23] Initial draft EV-D68 / EV-A71 3C Protease Assay Cascade [Assay Cascade] Assay cascade for EV-D68 / EV-A71 3C Protease oral antiviral Contributing Projects and Cores: Project 3 Project 5 Biochemical Assay Core Structural Biology Core Antiviral Core [2022-07-14] Initial draft Assay cascade for SARS-CoV-2 nsp3 Mac1 macrodomain oral antiviral [Assay Cascade (fragment-to-lead)] Partial SARS-CoV-2 nsp3 Mac1 macrodomain assay cascade for lead nomination Contributing Projects and Cores: Project 3 Project 5 Biochemical Assay Core Structural Biology Core Antiviral Core [2022-06-01] Initial draft Assay cascade for SARS-CoV-2 Mpro oral antiviral [Assay Cascade (lead optimization)] Assay cascade for lead optimization campaign for SARS-CoV-2 noncovalent oral inhibitor from the COVID Moonshot [2020-03-23] Initial draft for COVID Moonshot</description></item><item><title>Assay Protocols</title><link>https://asapdiscovery.org/outputs/assay-protocols/</link><pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate><guid>https://asapdiscovery.org/outputs/assay-protocols/</guid><description>ASAP frequently needs to develop or scale its own biochemical assay protocols to drive discovery programs. Whenever possible, we share these protocols through protocols.io, an industry standard platform for sharing and annotating assay protocols.
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href=/css/font.css rel=stylesheet type=text/css><link href=/css/kube.css rel=stylesheet type=text/css><link href=/css/kube.legenda.css rel=stylesheet type=text/css><link href=/css/highlight.css rel=stylesheet type=text/css><link href=/css/master.css rel=stylesheet type=text/css><link href=/css/kube.demo.css rel=stylesheet type=text/css><link href=/css/custom.css rel=stylesheet type=text/css><script src=/js/jquery-2.1.4.min.js type=text/javascript></script><script type=text/javascript src=/js/tocbot.min.js></script></head><body class=page-kube><header><div class=show-sm><div id=nav-toggle-box><div id=nav-toggle-brand><a href=/>ASAP Discovery Consortium</a></div><a data-component=toggleme data-target=#top href=# id=nav-toggle><i class=kube-menu></i></a></div></div><div class=hide-sm id=top><div id=top-brand><a href=/ title=home>ASAP Discovery Consortium</a></div><nav id=top-nav-main><ul><li><a href=/pipeline/>Pipeline</a></li><li><a href=/outputs/>Outputs</a></li><li><a href=https://www.choderalab.org/news/2021/10/26/asap-avidd-proposal>Concept</a></li><li><a href=/members/>Members</a></li><li><a href=/sab/>SAB</a></li><li><a href=/faq/>FAQ</a></li><li><a href=/awards/>Awards</a></li><li><a href=/forum/>Open Science Forum</a></li><li><a href=https://postera.ai/moonshot/>COVID Moonshot</a></li></ul></nav><nav id=top-nav-extra><ul></ul></nav></div></header><main><div id=main><div id=hero><h1>Software</h1><p class=hero-lead></p><div class="message error" data-component=message>This page is still in development. Please report any issues to <a href=https://github.com/asapdiscovery/asapdiscovery.github.io/issues>our issue tracker</a>.</div></div><div id=kube-component class=content><nav id=contents><ol class=js-toc></ol></nav><script type=text/javascript>document.addEventListener("DOMContentLoaded",function(){tocbot.init({tocSelector:".js-toc",contentSelector:".content",headingSelector:"h3"})})</script><p>Software produced by ASAP.</p><div class=prettybox data-component=prettybox><h3 style=text-align:left id=argos>argos</h3><a href=https://github.com/asapdiscovery/argos>[GitHub]</a><br>A web-based visualization tool for viewing DMS data on protein structures that allows users to generate and share these views using a web UI. See &lsquo;choppa&rsquo; package below.<br>Contributing Projects and Cores:
+<span class="label focus">Project 2</span>
+<span class="label focus">Computational Chemistry Core</span><br></div><div class=prettybox data-component=prettybox><h3 style=text-align:left id=asapdiscovery>asapdiscovery</h3><a href=https://github.com/asapdiscovery/asapdiscovery>[GitHub]</a>
+<a href=https://asapdiscovery.readthedocs.io/en/latest>[Documentation]</a><br>Monorepository for running computational chemistry project support for ASAP&rsquo;s viral targets, including docking, free energy calculations, chemoinformatics and machine learning.<br>Contributing Projects and Cores:
+<span class="label focus">Project 5</span>
+<span class="label focus">Computational Chemistry Core</span><br></div><div class=prettybox data-component=prettybox><h3 style=text-align:left id=choppa>choppa</h3><a href=https://github.com/asapdiscovery/choppa>[GitHub]</a>
+<a href=https://choppa.readthedocs.io>[Documentation]</a><br>A Python library for visualizing Deep Mutational Scanning data and other fitness data directly onto protein structures to enable fitness-informed decision-making in medicinal chemistry workflows in P2-P5 of ASAP&rsquo;s drug discovery pipeline.<br>Contributing Projects and Cores:
+<span class="label focus">Project 1</span>
+<span class="label focus">Computational Chemistry Core</span><br></div><div class=prettybox data-component=prettybox><h3 style=text-align:left id=falcbot>falcbot</h3><a href=https://github.com/asapdiscovery/FALCBot>[GitHub]</a><br>A slack integration for running computational chemistry workflows that are developed by ASAP&rsquo;s computational chemistry core.<br>Contributing Projects and Cores:
+<span class="label focus">Project 5</span>
+<span class="label focus">Computational Chemistry Core</span><br></div><div class=prettybox data-component=prettybox><h3 style=text-align:left id=hindsight>hindsight</h3><a href=https://github.com/asapdiscovery/hindsight-public>[GitHub]</a><br>Generates and continuously updates statistics and graphs comparing computational chemistry predictions with gathered experimental data to aid in hit-to-lead and lead optimization campaigns.<br>Contributing Projects and Cores:
+<span class="label focus">Project 5</span>
+<span class="label focus">Computational Chemistry Core</span><br></div></div></div></main><footer></footer><script src=/js/kube.js type=text/javascript></script><script src=/js/kube.legenda.js type=text/javascript></script><script src=/js/master.js type=text/javascript></script></body></html>
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