Tranquillyzer: A Flexible Neural Network Framework for Structural Annotation and Demultiplexing of Long-Read Transcriptomes. #StructuralAnnotation #LongReads #Transcriptomics #Bioinformatics @biorxiv_bioinfo biorxiv.org/content/10.1101/…

Web-based GTalign: bridging speed and accuracy in protein structure analysis @NAR_Open 1. GTalign-web is a new web-based implementation of the GTalign algorithm that achieves high-accuracy protein structure alignments while maintaining fast runtimes, effectively bridging the long-standing trade-off between sensitivity and computational speed. 2. Benchmarking against Foldseek and DALI shows that GTalign-web delivers the highest rate of accurate alignments (measured by TM-score and GDT_TS), with runtimes significantly faster than DALI and only moderately slower than Foldseek. 3. GTalign-web is powered by a spatial index-driven search engine and supports batch alignment of multiple protein models, accepting inputs in PDB or mmCIF formats—including compressed archives—making it suitable for large-scale structural mining. 4. It offers interactive results through an NGL-based 3D viewer and MSAViewer for multiple structure alignments, with download options for superimposed models and machine-readable outputs in JSON format for downstream analysis. 5. The web server supports searches against diverse structure databases including PDB, SCOPe, ECOD, Swiss-Prot, UniRef30, and AlphaFold models from 48 reference proteomes—providing deep structural annotation capabilities even for uncharacterized proteins. 6. Case studies demonstrated GTalign-web’s ability to detect remote homologs and structural analogs with as little as 4% sequence identity, correctly identifying domain-level relationships missed by other tools like DALI. 7. The server uses GPU-accelerated backend architecture and supports asynchronous job submission with three concurrent job slots, ensuring responsive performance and scalability for both casual users and high-throughput workflows. 8. GTalign-web outperforms DALI in aligning full domain architectures, and unlike Foldseek, it does not compromise sensitivity to achieve speed—highlighting its ability to resolve challenging structural comparisons in functional genomics and drug discovery. 9. The platform’s modular backend and frontend components are open-source and accessible via GitHub, along with benchmarking datasets and scripts, fostering reproducibility and community-driven development. 10. GTalign-web fills a key gap in the protein structure alignment landscape by offering both accuracy and speed at scale—an essential capability for interpreting the explosion of predicted protein structures from AlphaFold and related resources. 💻Code: github.com/minmarg/gtalign-w… github.com/chemikeris/comer_… github.com/minmarg/gtalign-w… 📜Paper: academic.oup.com/nar/advance… #ProteinStructure #StructuralBioinformatics #GTalign #AlphaFold #PDB #ProteinAlignment #Foldseek #DALI #DrugDiscovery #StructuralAnnotation #Bioinformatics #WebTools

d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes. #GeneticVariants #StructuralAnnotation #DockerContainer #Bioinformatics @GigaScience academic.oup.com/gigascience…