Research graph
References from Domain classification of archaeal proteomes reveals conserved fold repertoire. Local targets link to admitted publications; unresolved targets remain external evidence.
ECOD: an evolutionary classification of protein domains
10.1371/journal.pcbi.1003926 · 2014 · External reference
ECOD: new developments in the evolutionary classification of domains
10.1093/nar/gkw1137 · 2017 · External reference
ECOD: integrating classifications of protein domains from experimental and predicted structures
10.1093/nar/gkae1029 · 2025 · External reference
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya
10.1073/pnas.87.12.4576 · 1990 · External reference
Phylogenomics provides robust support for a two-domains tree of life
10.1038/s41559-019-1040-x · 2020 · External reference
AlphaFold protein structure database in 2024: providing structure coverage for over 214 million protein sequences
10.1093/nar/gkad1011 · 2024 · External reference
Expanded diversity of Asgard archaea and their relationships with eukaryotes
10.1038/s41586-021-03494-3 · 2021 · External reference
Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life
10.1126/science.aaf3883 · 2017 · External reference
Insights into the phylogeny and coding potential of microbial dark matter
10.1038/nature12352 · 2013 · External reference
Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling
10.1016/j.cub.2015.01.014 · 2015 · External reference
Archaea--timeline of the third domain
10.1038/nrmicro2482 · 2011 · External reference
Diversity, ecology and evolution of Archaea
10.1038/s41564-020-0715-z · 2020 · External reference
Archaea in coastal marine environments
10.1073/pnas.89.12.5685 · 1992 · External reference
Archaea and the human gut: new beginning of an old story
10.3748/wjg.v20.i43.16062 · 2014 · External reference
Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes
10.1371/journal.pcbi.1003009 · 2013 · External reference
Navigating the archaeal frontier: insights and projections from bioinformatic pipelines
10.3389/fmicb.2024.1433224 · 2024 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
DPAM: a domain parser for AlphaFold models
10.1002/pro.4548 · 2023 · External reference
Highly accurate protein structure prediction for the human proteome
10.1038/s41586-021-03828-1 · 2021 · External reference
ECOD domain classification of 48 whole proteomes from AlphaFold structure database using DPAM2
10.1371/journal.pcbi.1011586 · 2024 · External reference
Fast and accurate protein structure search with Foldseek
10.1038/s41587-023-01773-0 · 2024 · External reference
Genomic evidence for two functionally distinct gene classes
10.1073/pnas.95.11.6239 · 1998 · External reference
Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling
10.1038/s41564-026-02273-y · 2026 · External reference
Asgard archaea defense systems and their roles in the origin of eukaryotic immunity
10.1038/s41467-024-50195-2 · 2024 · External reference
Unresolved reference
2025 · External reference
Unresolved reference
2024 · External reference
Structural classification of zinc fingers: survey and summary
10.1093/nar/gkg161 · 2003 · External reference
DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites
10.1093/nar/gkm176 · 2007 · External reference
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing
10.1186/1745-6150-8-15 · 2013 · External reference
The in situ structure of T-series T1 reveals a conserved lambda-like tail tip
10.3390/v17030351 · 2025 · External reference
The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold
10.1016/s0968-0004(98)01189-x · 1998 · External reference
Structural aspects of the metzincin clan of metalloendopeptidases
10.1385/mb:24:2:157 · 2003 · External reference
The impact of structural genomics: expectations and outcomes
10.1126/science.1121018 · 2006 · External reference
The PDB is a covering set of small protein structures
10.1016/j.jmb.2003.10.027 · 2003 · External reference
Nature of the protein universe
10.1073/pnas.0905029106 · 2009 · External reference
Estimating the total number of protein folds
10.1002/(sici)1097-0134(19990601)35:4<408::aid-prot4>3.0.co;2-a · 1999 · External reference
Estimating the number of protein folds and families from complete genome data
10.1006/jmbi.2000.3786 · 2000 · External reference
A unifold, mesofold, and superfold model of protein fold use
10.1002/prot.10011 · 2002 · External reference
Unresolved reference
2022 · External reference
Prodigal: prokaryotic gene recognition and translation initiation site identification
10.1186/1471-2105-11-119 · 2010 · External reference
HH-suite3 for fast remote homology detection and deep protein annotation
10.1186/s12859-019-3019-7 · 2019 · External reference
Uniclust databases of clustered and deeply annotated protein sequences and alignments
10.1093/nar/gkw1081 · 2017 · External reference
Using dali for protein structure comparison
10.1007/978-1-0716-0270-6_3 · 2020 · External reference
Accelerated profile HMM searches
2011 · External reference
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
10.1038/nbt.3988 · 2017 · External reference
Estimating the total number of protein folds
10.1002/(sici)1097-0134(19990601)35:4<408::aid-prot4>3.0.co;2-a · ExternalCitation · doi-reference
DPAM: a domain parser for AlphaFold models
10.1002/pro.4548 · ExternalCitation · doi-reference
A unifold, mesofold, and superfold model of protein fold use
10.1002/prot.10011 · ExternalCitation · doi-reference
Estimating the number of protein folds and families from complete genome data
10.1006/jmbi.2000.3786 · ExternalCitation · doi-reference
Using dali for protein structure comparison
10.1007/978-1-0716-0270-6_3 · ExternalCitation · doi-reference
Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling
10.1016/j.cub.2015.01.014 · ExternalCitation · doi-reference
The PDB is a covering set of small protein structures
10.1016/j.jmb.2003.10.027 · ExternalCitation · doi-reference
The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold
10.1016/s0968-0004(98)01189-x · ExternalCitation · doi-reference
Insights into the phylogeny and coding potential of microbial dark matter
10.1038/nature12352 · ExternalCitation · doi-reference
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
10.1038/nbt.3988 · ExternalCitation · doi-reference
Archaea--timeline of the third domain
10.1038/nrmicro2482 · ExternalCitation · doi-reference
Asgard archaea defense systems and their roles in the origin of eukaryotic immunity
10.1038/s41467-024-50195-2 · ExternalCitation · doi-reference
Phylogenomics provides robust support for a two-domains tree of life
10.1038/s41559-019-1040-x · ExternalCitation · doi-reference
Diversity, ecology and evolution of Archaea
10.1038/s41564-020-0715-z · ExternalCitation · doi-reference
Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling
10.1038/s41564-026-02273-y · ExternalCitation · doi-reference
Expanded diversity of Asgard archaea and their relationships with eukaryotes
10.1038/s41586-021-03494-3 · ExternalCitation · doi-reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · ExternalCitation · doi-reference
Highly accurate protein structure prediction for the human proteome
10.1038/s41586-021-03828-1 · ExternalCitation · doi-reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · ExternalCitation · doi-reference
Fast and accurate protein structure search with Foldseek
10.1038/s41587-023-01773-0 · ExternalCitation · doi-reference
Nature of the protein universe
10.1073/pnas.0905029106 · ExternalCitation · doi-reference
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya
10.1073/pnas.87.12.4576 · ExternalCitation · doi-reference
Archaea in coastal marine environments
10.1073/pnas.89.12.5685 · ExternalCitation · doi-reference
Genomic evidence for two functionally distinct gene classes
10.1073/pnas.95.11.6239 · ExternalCitation · doi-reference
AlphaFold protein structure database in 2024: providing structure coverage for over 214 million protein sequences
10.1093/nar/gkad1011 · ExternalCitation · doi-reference
ECOD: integrating classifications of protein domains from experimental and predicted structures
10.1093/nar/gkae1029 · ExternalCitation · doi-reference
Structural classification of zinc fingers: survey and summary
10.1093/nar/gkg161 · ExternalCitation · doi-reference
DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites
10.1093/nar/gkm176 · ExternalCitation · doi-reference
Uniclust databases of clustered and deeply annotated protein sequences and alignments
10.1093/nar/gkw1081 · ExternalCitation · doi-reference
ECOD: new developments in the evolutionary classification of domains
10.1093/nar/gkw1137 · ExternalCitation · doi-reference
The impact of structural genomics: expectations and outcomes
10.1126/science.1121018 · ExternalCitation · doi-reference
Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life
10.1126/science.aaf3883 · ExternalCitation · doi-reference
Prodigal: prokaryotic gene recognition and translation initiation site identification
10.1186/1471-2105-11-119 · ExternalCitation · doi-reference
Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing
10.1186/1745-6150-8-15 · ExternalCitation · doi-reference
HH-suite3 for fast remote homology detection and deep protein annotation
10.1186/s12859-019-3019-7 · ExternalCitation · doi-reference
Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes
10.1371/journal.pcbi.1003009 · ExternalCitation · doi-reference
ECOD: an evolutionary classification of protein domains
10.1371/journal.pcbi.1003926 · ExternalCitation · doi-reference
ECOD domain classification of 48 whole proteomes from AlphaFold structure database using DPAM2
10.1371/journal.pcbi.1011586 · ExternalCitation · doi-reference
Structural aspects of the metzincin clan of metalloendopeptidases
10.1385/mb:24:2:157 · ExternalCitation · doi-reference
Navigating the archaeal frontier: insights and projections from bioinformatic pipelines
10.3389/fmicb.2024.1433224 · ExternalCitation · doi-reference
The in situ structure of T-series T1 reveals a conserved lambda-like tail tip
10.3390/v17030351 · ExternalCitation · doi-reference
Archaea and the human gut: new beginning of an old story
10.3748/wjg.v20.i43.16062 · ExternalCitation · doi-reference