ArticleBioinformatics (Oxford, England)2024
Chainsaw: protein domain segmentation with fully convolutional neural networks.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed.
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- pLM-Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection.Protein science : a publication of the Protein Society · 2026Article
- AI-enabled protein design facilitates future plant research and crop breeding.Plant physiology · 2026Review
- CASP16 Protein Monomer Structure Prediction Assessment.Proteins · 2026Article
- Divergent viral phosphodiesterases for immune signaling evasion.Cell host & microbe · 2025Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- OsmoFold: A high-throughput tool for predicting the impact of osmolytes on protein structure.Biophysical journal · 2025Article
- AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures.Bioinformatics (Oxford, England) · 2025Article
- Zero-shot segmentation using embeddings from a protein language model identifies functional regions in the human proteome.PLoS computational biology · 2025Article
- SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains.Bioinformatics (Oxford, England) · 2025Article
- FlatProt: 2D visualization eases protein structure comparison.BMC bioinformatics · 2025Article
- Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning.Bioinformatics (Oxford, England) · 2025Article
- Slice'N'Dice: maximizing the value of predicted models for structural biologists.Acta crystallographica. Section D, Structural biology · 2025Article
- Structural basis for cooperative ssDNA binding by bacteriophage protein filament P12.Nucleic acids research · 2025Article
- Selective utilization of medicinal polysaccharides by human gut Bacteroides and Parabacteroides species.Nature communications · 2025Article
- Fast protein structure searching using structure graph embeddings.Bioinformatics advances · 2025Article
- Semi-supervised segmentation of RNA 3D structures using density-based clustering.Computational and structural biotechnology journal · 2025Article
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Authors and funding
6 authors.
Funding
Abstract
motivationProtein domains are fundamental units of protein structure and play a pivotal role in understanding folding, function, evolution, and design. The advent of accurate structure prediction techniques has resulted in an influx of new structural data, making the partitioning of these structures into domains essential for inferring evolutionary relationships and functional classification.
resultsThis article presents Chainsaw, a supervised learning approach to domain parsing that achieves accuracy that surpasses current state-of-the-art methods. Chainsaw uses a fully convolutional neural network which is trained to predict the probability that each pair of residues is in the same domain. Domain predictions are then derived from these pairwise predictions using an algorithm that searches for the most likely assignment of residues to domains given the set of pairwise co-membership probabilities. Chainsaw matches CATH domain annotations in 78% of protein domains versus 72% for the next closest method. When predicting on AlphaFold models, expert human evaluators were twice as likely to prefer Chainsaw's predictions versus the next best method. AVAILABILITY AND IMPLEMENTATION: github.com/JudeWells/Chainsaw.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.