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SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning

Nucleic Acids Research(2021)10.1093/nar/gkab1054Source: DataRank Database

SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning is a dataset published in Nucleic Acids Research (2021). On theSindex it has a DataRank of 4.6, placing it in the top 4.7% of the data-sharing corpus. It has been cited 206 times, with 100 citing works in its 1-hop citation network.

Top 5%percentile

4.6DataRank

Ranks in the top 5% for downstream scientific impact

Data paper Open Access206 citations · 100 citing works in its network

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DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?

›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (5 grants)Impact (FWCI 10.00)OA: goldTopics (60)IDs (PubMed, PMC, OpenAlex)SDGs (1)

FAIR Checklist

Context only (not used in score)

Findable (1/2)

Has DOI

Accessible (1/2)

Open Access

Interoperable (0/2)

Reusable (1/3)

Dataset classification

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DataRank Breakdown

Base Score 17%Citation Network 83%

Base Score Contribution

0.800

From this paper's citation signal

Citation Network Contribution

3.8

From 100 citing papers with measurable signal

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Top 5 citers driving the network score

Ranked by each citer's contribution to N(p) — log1p(C_q) divided by its reference count — out of 100 citers.

Improved protein binder design using beta-pairing targeted RFdiffusion
bioRxiv (Cold Spring Harbor Laboratory)202417 citations4 referencesContributes 0.723
Chainsaw: protein domain segmentation with fully convolutional neural networks
Bioinformatics202445 citations27 referencesContributes 0.142
SWORD2: hierarchical analysis of protein 3D structures
Nucleic Acids Research202244 citations39 referencesContributes 0.098
Chainsaw: protein domain segmentation with fully convolutional neural networks
bioRxiv (Cold Spring Harbor Laboratory)202315 citations29 referencesContributes 0.096
The geometry of hidden representations of protein language models
bioRxiv (Cold Spring Harbor Laboratory)202211 citations26 referencesContributes 0.096

Authors (6)

Lindsey Guan ORCID,Shiangyi Lin ORCID,Changhua Yu ORCID,Naomi K. Fox ORCID,Steven E. Brenner ORCID

Live enrichment

PubMed:34850923 PMC:PMC8728185 OpenAlex:https://openalex.org/W3215918380

National Institutes of Health

Grant: R01-GM073109

U.S. Department of Energy

Grant: DE-AC02-05CH11231

NIGMS NIH HHS

Grant: R01 GM073109

National Institutes of Health

Grant: 5K15DE000205-03

CORRELATIVE CONSTRAINTS OF DIET, MORPHOLOGY AND BEHAVIOR

National Institutes of Health

Grant: 5R01GM073109-03

ASTRAL: Foundation for structure and evolution studies

FWCI

10.00

Citation Percentile

1.0%

Citation Trend

2022

2023

2024

2025

2026

goldLicense: cc-by

journalhttps://academic.oup.com/nar/article-pdf/50/D1/D553/42058119/gkab1054.pdf

publisherhttps://academic.oup.com/nar/article-pdf/50/D1/D553/42058119/gkab1054.pdf

journalhttps://doi.org/10.1093/nar/gkab1054

repositoryhttps://pubmed.ncbi.nlm.nih.gov/34850923

repositoryhttps://escholarship.org/uc/item/4r52p53p

Fields of Study

Genomics and Phylogenetic StudiesMachine Learning in BioinformaticsRNA and protein synthesis mechanisms0301 basic medicine03 medical and health sciences0303 health sciencesAlgorithmsComputational BiologyDatabases, ChemicalDatabases, ProteinGene Expression RegulationMachine LearningProteins

MeSH Terms

Machine LearningAlgorithmsGene Expression RegulationProteinsComputational BiologyDatabases, ProteinDatabases, Chemical

Keywords

Scope (computer science)Protein Data Bank (RCSB PDB)Structural Classification of Proteins databaseBiologyProtein Data BankComputational biologyComputer scienceInterpretation (philosophy)Protein structure databaseArtificial intelligenceMachine learningInformation retrievalBioinformaticsDatabaseProtein structureSequence databaseGeneticsProgramming languageGeneBiochemistry570572Bioinformatics and Computational BiologyChemicalDatabasesInformation and Computing SciencesMachine Learning and Artificial IntelligenceDatabase IssueDatabases, ProteinProteinProteinsBiological SciencesEnvironmental sciencesChemical sciencesGene Expression RegulationBiochemistry and Cell BiologyAlgorithmsDatabases, ChemicalBiotechnologyDevelopmental Biology

Sustainable Development Goals

SDG 0: Quality Education