ArticleNucleic acids research2022
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
88 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Tandem-repeat lectins: structural and functional insights.Glycobiology · 2024Pooled it
- Compositionally Biased Regions Within Structured Protein Domains.Biomolecules · 2026Article
- Nature Counts to Three: Universal Mg-Pinch Motif Polarizes the Cleaved Bond in NTP-Processing Enzymes.Journal of the American Chemical Society · 2026Article
- SplitSeek-Pro: accurate prediction of splittable sites on protein structures.Nature communications · 2026Article
- Structure-Based Comparative Analysis Reveals the Landscape of Powdery Mildew Secretomes Across Five Genera.Pathogens (Basel, Switzerland) · 2026Article
- Structural motif search across the protein universe with Folddisco.Nature biotechnology · 2026Article
- Mechanistic insights on spatiotemporal control of Ras-signaling.Biological chemistry · 2026Review
- Toward the regularization of E value from BLAST similarity search into a dissimilarity measure as distance function, and the metrication of protein sequence space.Briefings in bioinformatics · 2026Article
- A composition-matching algorithm, MatchIDR, identifies prion-like domains that localize to stress granules.Protein science : a publication of the Protein Society · 2026Article
- Identification of hot spring Obelisk-like RNA replicons and expanded diversity of the Obelisk superfamily.Nature communications · 2026Article
- Functional protein design and enhancement with ontology reinforcement iteration.Nature communications · 2026Article
- Crystal structure of plant γ-glutamyl peptidase 1: implications for sulfur metabolism and secondary metabolite biosynthesis.The FEBS journal · 2026Article
- Multi-scale structural similarity embedding search across entire proteomes.Bioinformatics (Oxford, England) · 2026Article
- CysDuF database: annotation and characterization of cysteine residues in domain of unknown function proteins based on cysteine post-translational modifications, their protein microenvironments, biochemical pathways, taxonomy, and diseases.Database : the journal of biological databases and curation · 2026Article
- Improved protein binder design using β-pairing targeted RFdiffusion.Nature communications · 2026Article
- Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments.Genome biology and evolution · 2026Article
- Development of molecular biomarkers for monitoring of arable crops colonization withFrontiers in plant science · 2026Article
- Network of interactions between the tumor necrosis factor superfamily members and small S100 proteins.PloS one · 2026Article
- From CASP13 to the Nobel Prize: DeepMind's AlphaFold Journey in Revolutionizing Protein Structure Prediction and Beyond.Current protein & peptide science · 2026Review
- A Conserved Planthopper MATH-BTB Protein Regulates Fecundity inInternational journal of molecular sciences · 2025Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The Structural Classification of Proteins-extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst the majority of proteins of known structure, along with resources for analyzing the protein structures and their sequences. Structures from the PDB are divided into domains and classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.08, we have developed search and display tools for analysis of genetic variants we mapped to structures classified in SCOPe. In order to improve the utility of SCOPe to automated methods such as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins, we have introduced new machine-parseable annotations that indicate aberrant structures as well as domains that are distinguished by a smaller repeat unit. We also classified structures from 74 of the largest Pfam families not previously classified in SCOPe, and we improved our algorithm to remove N- and C-terminal cloning, expression and purification sequences from SCOPe domains. SCOPe 2.08-stable classifies 106 976 PDB entries (about 60% of PDB entries).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.