ArticleBriefings in bioinformatics2021
Topoly: Python package to analyze topology of polymers.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it.
- How soluble misfolded proteins bypass chaperones at the molecular level.Nature communications · 2023Pooled it
- Protein entanglement misfolding influences whether proteins undergo proteasomal degradation or persist in near-native misfolded states.Nature communications · 2026Article
- Novel Knotted Solenoid fold with order-shifted coil arrangement leads to nontrivial 3Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Natively entangled proteins are linked to human disease and pathogenic mutations likely due to a greater misfolding propensity.bioRxiv : the preprint server for biology · 2026Article
- Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data.bioRxiv : the preprint server for biology · 2026Article
- Native entanglement misfolding contributes to age-associated structural changebioRxiv : the preprint server for biology · 2026Article
- Topological data analysis and topological deep learning beyond persistent homology: a review.Artificial intelligence review · 2026Article
- A widespread protein misfolding mechanism is differentially rescued in vitro by chaperones based on gene essentiality.Nature communications · 2025Article
- A widespread protein misfolding mechanism is differentially rescued by chaperones based on gene essentiality.bioRxiv : the preprint server for biology · 2025Article
- Link node: A method to characterize the chain topology of intrinsically disordered proteins.Quantitative biology (Beijing, China) · 2025Article
- AlphaLasso-a web server to identify loop and lasso motifs in 3D structure of biopolymers.Nucleic acids research · 2025Article
- Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.Nature communications · 2025Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- Protein misfolding involving entanglements providesa structural explanation for the origin of stretched-exponential refolding kinetics.Science advances · 2025Article
- Unknotting RNA: A method to resolve computational artifacts.PLoS computational biology · 2025Article
- Knot data analysis using multiscale Gauss link integral.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Theta-curves in proteins.Protein science : a publication of the Protein Society · 2024Article
- AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.Nucleic acids research · 2024Article
- Knot or not? Identifying unknotted proteins in knotted families with sequence-based Machine Learning model.Protein science : a publication of the Protein Society · 2024Article
- Knotted artifacts in predicted 3D RNA structures.PLoS computational biology · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increasing role of topology in (bio)physical properties of matter creates a need for an efficient method of detecting the topology of a (bio)polymer. However, the existing tools allow one to classify only the simplest knots and cannot be used in automated sample analysis. To answer this need, we created the Topoly Python package. This package enables the distinguishing of knots, slipknots, links and spatial graphs through the calculation of different topological polynomial invariants. It also enables one to create the minimal spanning surface on a given loop, e.g. to detect a lasso motif or to generate random closed polymers. It is capable of reading various file formats, including PDB. The extensive documentation along with test cases and the simplicity of the Python programming language make it a very simple to use yet powerful tool, suitable even for inexperienced users. Topoly can be obtained from https://topoly.cent.uw.edu.pl.
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