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The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures

https://doi.org/10.1093/nar/gkz1064
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/jmbi.2001.5080openalex-snapshot
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
inferredcites →https://doi.org/10.1016/j.str.2012.01.024openalex-snapshot
Detection of Spatial Correlations in Protein Structures and Molecular Complexes
inferredcites →https://doi.org/10.1016/s0022-2836(05)80134-2openalex-snapshot
SCOP: A structural classification of proteins database for the investigation of sequences and structures
inferredcites →https://doi.org/10.1038/s41594-017-0019-zopenalex-snapshot
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inferredcites →https://doi.org/10.1073/pnas.1208134110openalex-snapshot
Structural basis for Zn 2+ -dependent intercellular adhesion in staphylococcal biofilms
inferredcites →https://doi.org/10.1074/jbc.m109.010983openalex-snapshot
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inferredcites →https://doi.org/10.1093/bioinformatics/btg1086openalex-snapshot
Flexible structure alignment by chaining aligned fragment pairs allowing twists
inferredcites →https://doi.org/10.1093/bioinformatics/bty419openalex-snapshot
NGL viewer: web-based molecular graphics for large complexes
inferredcites →https://doi.org/10.1093/nar/gkh034openalex-snapshot
The ASTRAL Compendium in 2004
inferredcites →https://doi.org/10.1093/nar/gkt1240openalex-snapshot
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
inferredcites →https://doi.org/10.1093/nar/gkt1242openalex-snapshot
SCOP2 prototype: a new approach to protein structure mining
inferredcites →https://doi.org/10.1093/nar/gkw1098openalex-snapshot
CATH: an expanded resource to predict protein function through structure and sequence
inferredcites →https://doi.org/10.1093/nar/gkw357openalex-snapshot
Dali server update
inferredcites →https://doi.org/10.1093/nar/gky1049openalex-snapshot
UniProt: a worldwide hub of protein knowledge
inferredcites →https://doi.org/10.1093/nar/gky1114openalex-snapshot
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins
inferredcites →https://doi.org/10.1093/nar/gky1124openalex-snapshot
The European Bioinformatics Institute in 2018: tools, infrastructure and training
inferredcites →https://doi.org/10.1093/nar/gky1130openalex-snapshot
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver
inferredcites →https://doi.org/10.1093/nar/gky949openalex-snapshot
Protein Data Bank: the single global archive for 3D macromolecular structure data
inferredcites →https://doi.org/10.1093/nar/gky995openalex-snapshot
The Pfam protein families database in 2019
inferredcites →https://doi.org/10.1126/science.1144706openalex-snapshot
A Common Fold Mediates Vertebrate Defense and Bacterial Attack
inferredcites →https://doi.org/10.1371/journal.pbio.1002049openalex-snapshot
Conformational Changes during Pore Formation by the Perforin-Related Protein Pleurotolysin
inferredcites →https://doi.org/10.1371/journal.pcbi.1003926openalex-snapshot
ECOD: An Evolutionary Classification of Protein Domains
inferredcites →https://doi.org/10.1371/journal.pone.0024790openalex-snapshot
Structure and Molecular Evolution of CDGSH Iron-Sulfur Domains

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inferred← citeshttps://doi.org/10.1002/1873-3468.14856openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/cpz1.70018openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/iub.2911openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4192openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4213openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4277openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4301openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4465openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.4482openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/pro.70586openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/prot.26089openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-2095-3_3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-2974-1_1openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-2974-1_5openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-4213-9_1openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-4213-9_18openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-4662-5_12openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00144-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-323-95502-7.00187-1openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.str.2023.04.003openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.str.2025.07.005openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.tim.2020.08.003openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.biochem.2c00640openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.1c01335openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01139openalex-snapshot
IntEnzyDB: an Integrated Structure–Kinetics Enzymology Database
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01405openalex-snapshot
PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00599openalex-snapshot
The Systematic Study of Spatially Conserved Salt Bridges in Protein
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.3c00352openalex-snapshot
Structural Insights into Molecular Recognition and Receptor Activation in Chemokine–Chemokine Receptor Complexes
inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c05367openalex-snapshot
Number of Hydrogen Bonds per Unit Solvent Accessible Surface Area: A Descriptor of Functional States of Proteins
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c04958openalex-snapshot
Appraisal of blob-Based Approaches in the Prediction of Protein Folding Times
inferred← citeshttps://doi.org/10.1021/acsomega.1c00950openalex-snapshot
Completeness and Consistency in Structural Domain Classifications
inferred← citeshttps://doi.org/10.1021/acsomega.2c05881openalex-snapshot
Improved Prediction Model of Protein and Peptide Toxicity by Integrating Channel Attention into a Convolutional Neural Network and Gated Recurrent Units
inferred← citeshttps://doi.org/10.1021/jacsau.3c00749openalex-snapshot
Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines
inferred← citeshttps://doi.org/10.1038/s41467-022-33004-6openalex-snapshot
De novo design of immunoglobulin-like domains
inferred← citeshttps://doi.org/10.1038/s41467-023-41664-1openalex-snapshot
Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models
inferred← citeshttps://doi.org/10.1038/s41467-023-43934-4openalex-snapshot
Merizo: a rapid and accurate protein domain segmentation method using invariant point attention
inferred← citeshttps://doi.org/10.1038/s41467-024-50730-1openalex-snapshot
Structural basis of tRNA recognition by the widespread OB fold
inferred← citeshttps://doi.org/10.1038/s41467-026-69673-wopenalex-snapshot
Allosteric and energetic remodeling of a PDZ domain by protein domain extensions
inferred← citeshttps://doi.org/10.1038/s41522-021-00220-9openalex-snapshot
Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome
inferred← citeshttps://doi.org/10.1038/s41561-022-01053-7openalex-snapshot
Declining metal availability in the Mesozoic seawater reflected in phytoplankton succession
inferred← citeshttps://doi.org/10.1038/s41586-021-03828-1openalex-snapshot
Highly accurate protein structure prediction for the human proteome
inferred← citeshttps://doi.org/10.1038/s41586-023-06583-7openalex-snapshot
Unraveling the functional dark matter through global metagenomics
inferred← citeshttps://doi.org/10.1038/s41586-024-07601-yopenalex-snapshot
Computational design of soluble and functional membrane protein analogues
inferred← citeshttps://doi.org/10.1038/s41586-024-08370-4openalex-snapshot
Site-saturation mutagenesis of 500 human protein domains
inferred← citeshttps://doi.org/10.1038/s41587-023-01917-2openalex-snapshot
Protein remote homology detection and structural alignment using deep learning
inferred← citeshttps://doi.org/10.1038/s41592-024-02272-zopenalex-snapshot
OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
inferred← citeshttps://doi.org/10.1038/s41594-021-00586-6openalex-snapshot
Synergies between the Protein Data Bank and the community
inferred← citeshttps://doi.org/10.1038/s41594-023-00920-0openalex-snapshot
The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity
inferred← citeshttps://doi.org/10.1038/s41594-025-01676-5openalex-snapshot
The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking
inferred← citeshttps://doi.org/10.1038/s41597-023-02101-6openalex-snapshot
Unified access to up-to-date residue-level annotations from UniProtKB and other biological databases for PDB data
inferred← citeshttps://doi.org/10.1038/s41597-024-03999-2openalex-snapshot
Quantum chemical calculation dataset for representative protein folds by the fragment molecular orbital method
inferred← citeshttps://doi.org/10.1038/s41598-023-39273-5openalex-snapshot
Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains
inferred← citeshttps://doi.org/10.1038/s41598-023-47496-9openalex-snapshot
A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins
inferred← citeshttps://doi.org/10.1038/s41598-023-50913-8openalex-snapshot
Conformational diversity and protein–protein interfaces in drug repurposing in Ras signaling pathway
inferred← citeshttps://doi.org/10.1038/s41598-024-71699-3openalex-snapshot
Teaching old docks new tricks with machine learning enhanced ensemble docking
inferred← citeshttps://doi.org/10.1038/s42003-022-03269-0openalex-snapshot
Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes
inferred← citeshttps://doi.org/10.1038/s42003-023-05076-7openalex-snapshot
Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon
inferred← citeshttps://doi.org/10.1038/s43588-023-00438-xopenalex-snapshot
Domain-agnostic predictions of nanoscale interactions in proteins and nanoparticles
inferred← citeshttps://doi.org/10.1038/s43588-023-00440-3openalex-snapshot
Score-based generative modeling for de novo protein design
inferred← citeshttps://doi.org/10.1038/s44222-025-00346-xopenalex-snapshot
Multi-dimensional metagenomics
inferred← citeshttps://doi.org/10.1042/bst20190712openalex-snapshot
The expanding world of protein kinase-like families in bacteria: forty families and counting
inferred← citeshttps://doi.org/10.1042/bst20220849openalex-snapshot
General strategies for using amino acid sequence data to guide biochemical investigation of protein function
inferred← citeshttps://doi.org/10.1063/4.0000251openalex-snapshot
Identifying protein conformational states in the Protein Data Bank: Toward unlocking the potential of integrative dynamics studies
inferred← citeshttps://doi.org/10.1073/pnas.2006332117openalex-snapshot
Structure of the RECK CC domain, an evolutionary anomaly
inferred← citeshttps://doi.org/10.1073/pnas.2214069120openalex-snapshot
Classification of domains in predicted structures of the human proteome
inferred← citeshttps://doi.org/10.1080/00275514.2024.2373665openalex-snapshot
Genome-wide search and gene expression studies reveal candidate effectors with a role in pathogenicity and virulence in Fusarium graminearum
inferred← citeshttps://doi.org/10.1080/07391102.2021.2017352openalex-snapshot
Protein–protein docking and molecular dynamics studies of sericin and cocoonase of silkworm: an insight for cocoon softening
inferred← citeshttps://doi.org/10.1080/07391102.2024.2328736openalex-snapshot
Machine learning-based prediction of proteins’ architecture using sequences of amino acids and structural alphabets
inferred← citeshttps://doi.org/10.1080/07391102.2024.2429798openalex-snapshot
Two groups and three classes of the conserved structural organization of nucleophile and non-canonical ElbowFlankOxy networks in different superfamily proteins
inferred← citeshttps://doi.org/10.1080/07391102.2024.2434033openalex-snapshot
Structural insights into the ATP-dependent activation of NOD-like receptor with pyrin 3 (NLRP3) protein by molecular dynamics simulation
inferred← citeshttps://doi.org/10.1080/17460441.2025.2557599openalex-snapshot
The structural basis of drugs targeting protein–protein interactions uncovered with the protein–ligand interaction profiler PLIP
inferred← citeshttps://doi.org/10.1093/aobpla/plad079openalex-snapshot
Transcriptome-based network analysis of cell cycle-related genes in response to blue and red light in maize
inferred← citeshttps://doi.org/10.1093/bfgp/elaf020openalex-snapshot
Computational inference of Rhizobium phaseoli transcriptional regulatory network predicts Transcription Factors involved in nodulation
inferred← citeshttps://doi.org/10.1093/bib/bbaa362openalex-snapshot
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies
inferred← citeshttps://doi.org/10.1093/bib/bbaa404openalex-snapshot
SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets
inferred← citeshttps://doi.org/10.1093/bib/bbad486openalex-snapshot
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency
inferred← citeshttps://doi.org/10.1093/bib/bbae146openalex-snapshot
SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition
inferred← citeshttps://doi.org/10.1093/bib/bbag293openalex-snapshot
ProtDML: label-aware representation learning for broad-spectrum protein function prediction
inferred← citeshttps://doi.org/10.1093/bioadv/vbab038openalex-snapshot
Secondary structure assignment of proteins in the absence of sequence information
inferred← citeshttps://doi.org/10.1093/bioadv/vbad081openalex-snapshot
CroMaSt: a workflow for assessing protein domain classification by cross-mapping of structural instances between domain databases and structural alignment
inferred← citeshttps://doi.org/10.1093/bioadv/vbae052openalex-snapshot
WAS IT A MATch I SAW? Approximate palindromes lead to overstated false match rates in benchmarks using reversed sequences
inferred← citeshttps://doi.org/10.1093/bioadv/vbae119openalex-snapshot
In the twilight zone of protein sequence homology: do protein language models learn protein structure?
inferred← citeshttps://doi.org/10.1093/bioadv/vbae132openalex-snapshot
Investigation of protein family relationships with deep learning
inferred← citeshttps://doi.org/10.1093/bioadv/vbae161openalex-snapshot
ProCogGraph: a graph-based mapping of cognate ligand domain interactions
inferred← citeshttps://doi.org/10.1093/bioadv/vbaf042openalex-snapshot
Fast protein structure searching using structure graph embeddings
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa833openalex-snapshot
Fold recognition by scoring protein maps using the congruence coefficient
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac020openalex-snapshot
ProteinBERT: a universal deep-learning model of protein sequence and function
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac121openalex-snapshot
localpdb—a Python package to manage protein structures and their annotations
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac159openalex-snapshot
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac242openalex-snapshot
Simulating domain architecture evolution
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac246openalex-snapshot
Bridging the gaps in statistical models of protein alignment
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