ArticleNucleic acids research2019
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
- M2-PRNet: multi-scale and multi-modal learning for protein-RNA binding affinity prediction.Bioinformatics (Oxford, England) · 2026Article
- Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER.Nature biotechnology · 2026Article
- Scalable homology detection with ERAST.Nature biotechnology · 2026Article
- CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin Evaluation.Interdisciplinary sciences, computational life sciences · 2026Article
- Enhancing protein structure prediction: evaluating the role of amino acid physicochemical features in homology search.Briefings in bioinformatics · 2026Article
- Using evolutionary context to classify difficult protein folds.PLoS computational biology · 2025Article
- Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules Versus Therapeutic Peptides.Biology · 2025Review
- Exploration of Comprehensive Structural and Functional Potential of Recombinant Proteins Using Cutting-Edge Bioinformatics Tools.Applied biochemistry and biotechnology · 2025Review
- SHREC 2025: Protein surface shape retrieval including electrostatic potential.Computers & graphics · 2025Article
- An interpretable alphabet for local protein structure search based on amino acid neighborhoods.Bioinformatics (Oxford, England) · 2025Article
- Recent advances in the inference of deep viral evolutionary history.Journal of virology · 2025Review
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- Web-based GTalign: bridging speed and accuracy in protein structure analysis.Nucleic acids research · 2025Article
- Fast, sensitive detection of protein homologs using deep dense retrieval.Nature biotechnology · 2025Article
- Cutting-edge deep-learning based tools for metagenomic research.National science review · 2025Review
- Fast protein structure searching using structure graph embeddings.Bioinformatics advances · 2025Article
- Bilingual language model for protein sequence and structure.NAR genomics and bioinformatics · 2024Article
- Protein engineering in the deep learning era.mLife · 2024Review
- Prediction of Protein Secondary Structures Based on Substructural Descriptors of Molecular Fragments.International journal of molecular sciences · 2024Article
13 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
The SCOPe (Structural Classification of Proteins-extended, https://scop.berkeley.edu) database hierarchically classifies domains from the majority of proteins of known structure according to their structural and evolutionary relationships. SCOPe also incorporates and updates the ASTRAL compendium, which provides multiple databases and tools to aid in the analysis of the sequences and structures of proteins classified in SCOPe. Protein structures are classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.07, we have focused our manual curation efforts on larger protein structures, including the spliceosome, proteasome and RNA polymerase I, as well as many other Pfam families that had not previously been classified. Domains from these large protein complexes are distinctive in several ways: novel non-globular folds are more common, and domains from previously observed protein families often have N- or C-terminal extensions that were disordered or not present in previous structures. The current monthly release update, SCOPe 2.07-2018-10-18, classifies 90 992 PDB entries (about two thirds of PDB entries).
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