ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data pubs.acs.org/doi/10.1021/acs… @esrehmki @GutermuthTorben #JCIM Vol66 Issue2 #ChemicalInformation

Enabling automatic generation of protein-ligand complex datasets with atomistic detail 1. A new study introduces StrAcTable, an automated dataset of annotated protein-ligand complexes, combining detailed structural data from PDB and bioactivity data from ChEMBL. This dataset aims to address the challenge of linking structural and bioactivity data, which is crucial for structure-based drug design. 2. StrAcTable includes 20,063 protein-ligand complexes with bioactivity values, derived from ChEMBL Version 35. The dataset provides detailed quality assessments of the matching between protein sequences and small molecules, as well as the overall structure quality. 3. The innovation lies in the fully automated workflow, which uses tools like ActivityFinder, LigandExtractor, and StructureProfiler to integrate and assess data quality. This automation allows for sustainable growth and updates, reducing manual efforts significantly. 4. StrAcTable offers multiple versions to cater to different research needs, including filtered datasets that retain only the best-matching ChEMBL targets. This flexibility makes it a valuable resource for both machine-learning and traditional docking-scoring development. 5. The study highlights the importance of sequence and molecule matching quality, categorizing matches into Gold, Silver, and Bronze levels. This allows researchers to filter data based on desired quality criteria. 6. StrAcTable also tracks mutations in the binding site, providing insights into potential influences on binding affinity. The dataset's chemical diversity and wide range of activity values make it a comprehensive resource for drug discovery projects. 7. The authors demonstrate the potential of StrAcTable by constructing high-quality datasets for specific targets, such as the Tyrosine protein kinase ABL. This showcases how StrAcTable can be used to create tailored datasets for individual research needs. 📜Paper: biorxiv.org/content/10.64898… 💻Code: github.com/rareylab/StrAcTab… #StrAcTable #ProteinLigandComplex #AutomatedDataset #DrugDiscovery #Bioactivity #StructureBasedDesign

ProteinsPlus: a publicly available resource for protein structure mining @NAR_Open 1. ProteinsPlus is an open-access web server offering a comprehensive suite of tools for protein structure analysis, protein-ligand modeling, and PDB mining—making it one of the most versatile resources for structure-based drug design. 2. The latest update introduces DoGSite3, a robust and orientation-invariant binding pocket predictor with ligand-biased mode, outperforming existing geometry-based tools in pocket detection speed and precision. 3. The GeoMine tool was enhanced with a novel 2D query interface, enabling users to define structural search templates from ligand-bound pockets using intuitive chemical diagrams while synchronizing with a 3D viewer for spatial accuracy. 4. PoseEdit, an upgraded 2D interaction diagram editor, allows interactive exploration and customization of protein-ligand binding modes, introducing new features like ionic and covalent bond detection, color gradients, and synchronized 3D mapping. 5. The new LifeSoaks module analyzes solvent channels in crystallographic structures, enabling researchers to assess accessibility of binding pockets in protein crystals, a key consideration in fragment soaking experiments. 6. ProteinsPlus supports PDB files, AlphaFold predictions, or user-uploaded structures as input, and provides programmatic REST API access and KNIME integration, allowing large-scale, automated workflows for high-throughput structural mining. 7. In a real-world application, the platform was used to mine CK1α binding pockets, perform similarity searches across the PDB using SIENA, assess ligand activity with ActivityFinder, and generate interaction diagrams with PoseEdit—all within a KNIME pipeline. 8. The server’s modular tools are now being redesigned using Django and Vue.js to improve scalability, interoperability, and long-term maintainability—enabling seamless tool chaining like GeoMine-to-SIENA query propagation. 9. From metal coordination (METALizer) and structure quality (StructureProfiler, EDIAscorer) to docking automation (JAMDA, Protoss), ProteinsPlus combines analysis, prediction, and mining tools into a single platform for novice and expert users alike. 10. By integrating cutting-edge visualization, interaction modeling, and automation features, ProteinsPlus empowers the structural biology and medicinal chemistry communities to efficiently extract actionable insights from protein structures. 💻Code: proteins.plus 📜Paper: academic.oup.com/nar/advance… #ProteinStructure #DrugDesign #BindingSitePrediction #ProteinsPlus #StructuralBiology #KNIME #Bioinformatics #LigandInteraction #Docking #WebTools #OpenScience

ProteinsPlus: a publicly available resource for protein structure mining @NAR_Open 1. ProteinsPlus is an open-access web server offering a comprehensive suite of tools for protein structure analysis, protein-ligand modeling, and PDB mining—making it one of the most versatile resources for structure-based drug design. 2. The latest update introduces DoGSite3, a robust and orientation-invariant binding pocket predictor with ligand-biased mode, outperforming existing geometry-based tools in pocket detection speed and precision. 3. The GeoMine tool was enhanced with a novel 2D query interface, enabling users to define structural search templates from ligand-bound pockets using intuitive chemical diagrams while synchronizing with a 3D viewer for spatial accuracy. 4. PoseEdit, an upgraded 2D interaction diagram editor, allows interactive exploration and customization of protein-ligand binding modes, introducing new features like ionic and covalent bond detection, color gradients, and synchronized 3D mapping. 5. The new LifeSoaks module analyzes solvent channels in crystallographic structures, enabling researchers to assess accessibility of binding pockets in protein crystals, a key consideration in fragment soaking experiments. 6. ProteinsPlus supports PDB files, AlphaFold predictions, or user-uploaded structures as input, and provides programmatic REST API access and KNIME integration, allowing large-scale, automated workflows for high-throughput structural mining. 7. In a real-world application, the platform was used to mine CK1α binding pockets, perform similarity searches across the PDB using SIENA, assess ligand activity with ActivityFinder, and generate interaction diagrams with PoseEdit—all within a KNIME pipeline. 8. The server’s modular tools are now being redesigned using Django and Vue.js to improve scalability, interoperability, and long-term maintainability—enabling seamless tool chaining like GeoMine-to-SIENA query propagation. 9. From metal coordination (METALizer) and structure quality (StructureProfiler, EDIAscorer) to docking automation (JAMDA, Protoss), ProteinsPlus combines analysis, prediction, and mining tools into a single platform for novice and expert users alike. 10. By integrating cutting-edge visualization, interaction modeling, and automation features, ProteinsPlus empowers the structural biology and medicinal chemistry communities to efficiently extract actionable insights from protein structures. 💻Code: proteins.plus 📜Paper: academic.oup.com/nar/advance… #ProteinStructure #DrugDesign #BindingSitePrediction #ProteinsPlus #StructuralBiology #KNIME #Bioinformatics #LigandInteraction #Docking #WebTools #OpenScience

If you have been inspired by the fantastic stories about Women and Girls getting active 🤾 ⬇️ ⚫ Check our Activity Finder ➡️ow.ly/xR0b50TEpG9 🔴Contact us to find the activity for you ➡️activityfinder@glasgowlife.org.uk @ActiveScotGov #SheCanSheWill #LetsMoveTogether

🌊🚣‍♀️ Inspired by #TheBoatRace to give #rowing a go? Take up a new challenge, the Thames is calling. Get afloat, enjoy the fresh air and explore London’s #BlueSpace. Check out our #ActivityFinder for rowing taster sessions hubs.la/Q02rd62W0 #ActiveThames #Fitness #Sport

What a win by the @Lionesses! 🏴󠁧󠁢󠁥󠁮󠁧󠁿 👏 Feeling inspired? Find your next physical activity session right here on Active Birmingham - activebirmingham.co.uk/ #Lionesses #England #ActivityFinder

Do you provide physical activity and sports opportunities for people in Kent? Add your details (for free) to our Activity Finder and help us build a comprehensive resource for our county. bit.ly/3XKm04A #Kent #Medway #PhysicalActivity #ActivityFinder

We’re updating our on-line sport & physical activity finder. Add your club or classes for free! 🤩 ✅ quick & easy to do ✅ can help you reach new members ✅ registration is free Add your club or classes using the link below 👇 tinyurl.com/53bpujnm #ActivityFinder #Cumbria

This month, we've wanted to share the many opportunities available to #Essex residents, to get active. Whether it's the more unusual activities such as #Bouldering or #AerialAerobics, we want to support you to #FindYourActive! Visit the #ActivityFinder: activeessex.org/activity-fin…

🌊🚣‍♀️ Inspired by #TheBoatRace to give #rowing a go? Take up a new challenge, the Thames is calling. Check out our #ActivityFinder to find rowing taster sessions hubs.la/Q01J8Dvn0 Get afloat, enjoy the fresh air and explore London’s #BlueSpace. #ActiveThames #Fitness

Being active can help release tension and works as a great mood booster! 😀 You can do it on your own, or in a team. Utilise our #ActivityFinder to find what is available near you 📍 ow.ly/PYa150Lt4q8 #StressAwarenessWeek

We've updated our #ActivityFinder page🎉 With new and improved filters, you can now select if you require an activity for a particular physical impairment, age range, level of activity fitness, length and size of class time, and price. Visit here: bit.ly/FYAActivityFinder

Exciting developments for #FindYourActive our #ActivityFinder has had a makeover! ✨ With new filter functions, menus and a clearer route to book on to classes, we hope that this will help more Essex residents to find what's right for them! Click here: bit.ly/FYAActivityFinder

Check out the free activities in Southgate thanks to @LondonSport's activityfinder. Let's get @ActiveEnfield with #NorthLondonHockey! getactive.activityfinder.net…

We've updated our #ActivityFinder to make it easier to find activities delivered by local providers in-person, or virtually. If you prefer to #StayInWorkOut (especially in the heat) why not join @MewsOrg or @GreenhouseSport for some zumba today at 11am: active.westminster.gov.uk

British Blind Sport launches #ActivityFinder! @BritBlindSport is pleased to announce the launch of their Activity Find, which is now live visionuk.org.uk/british-blin…

Have you seen the new activity finder from @ActiveCdale our classes are now on there check out our news post here waccic.com/2020/01/15/check-… #ActiveLifestyle #ActiveCalderdale #ActivityFinder #StayHealthy #StayActive #ActivitiesForAll #ChairBasedExercise calderdale.activityfinder.ne… 🚶‍♀️🚴‍♀️

Thanks for sharing our #ActivityFinder @EssexPH! We hope that it will inspire the people of #Essex to get physically active this #REDJanuary!

We’re looking for sport & activity providers that work with Early Years. If you’re one of them, please do add to our activity finder 👍activecumbria.org/addyouract… or if you know one reply & tag them in the thread #earlyyears #activetots #activekids #activityfinder #preschool #nursery