ArticleBioinformatics advances2023
pyScoMotif: discovery of similar 3D structural motifs across proteins.
Article in Bioinformatics advances, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Investigating enzyme function by geometric matching of catalytic motifs.Protein science : a publication of the Protein Society · 2026Article
- Human interferon stimulated genes target ancient features of animal and bacterial viral replication.bioRxiv : the preprint server for biology · 2026Article
- Structural motif search across the protein universe with Folddisco.Nature biotechnology · 2026Article
- ActSeek: fast and accurate search algorithm of active sites in alphafold database.Bioinformatics (Oxford, England) · 2025Article
- Functional and structural insights into α-L-Rhamnosidase: cloning, characterization, and decoding evolutionary constraints through structural motif.Archives of microbiology · 2025Article
- Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?Protein science : a publication of the Protein Society · 2024Article
- Sequence-Structure Analysis Unlocking the Potential Functional Application of the Local 3D Motifs of Plant-Derived Diterpene Synthases.Biomolecules · 2024Article
- An optimized relational database for querying structural patterns in proteins.Database : the journal of biological databases and curation · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: The fast and accurate detection of similar geometrical arrangements of protein residues, known as 3D structural motifs, is highly relevant for many applications such as binding region and catalytic site detection, drug discovery and structure conservation analyses. With the recent publication of new protein structure prediction methods, the number of available protein structures is exploding, which makes efficient and easy-to-use tools for identifying 3D structural motifs essential. Results: We present an open-source Python package that enables the search for both exact and mutated motifs with position-specific residue substitutions. The tool is efficient, flexible, accurate, and suitable to run both on computer clusters and personal laptops. Two successful applications of pyScoMotif for catalytic site identification are showcased. Availability and implementation: The pyScoMotif package can be installed from the PyPI repository and is also available at https://github.com/3BioCompBio/pyScoMotif. It is free to use for non-commercial purposes.
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Registered trials
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