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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.