FAIRsharing.a8z6gz; Last edited: April 26, 2021, 9:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

ProDom protein domain database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556

prodom
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556

Other names: ProDom protein domain database, prodom

This source may no longer be available. No known URL could be resolved successfully.

ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.

Webpage:

http://prodom.prabi.fr/

Licence:

Name: Prodom Database License
URL: http://prodom.prabi.fr/prodom/current/html/downcom.php

Publications:

Publications
More detailed information about this field from each metasource.

The ProDom database of protein domain families: more emphasis on 3D
PMID: 15608179
metasource: Fairsharing.org
version: FAIRsharing.org: ProDom; ProDom; DOI: https://doi.org/10.25504/FAIRsharing.a8z6gz; Last edited: April 26, 2021, 9:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

ProDom: automated clustering of homologous domains
PMID: 12230033
metasource: Fairsharing.org
version: FAIRsharing.org: ProDom; ProDom; DOI: https://doi.org/10.25504/FAIRsharing.a8z6gz; Last edited: April 26, 2021, 9:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

http://dx.doi.org/10.1093/nar/28.1.267
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556

The ProDom database of protein domain families: more emphasis on 3D PubMed citations: 151.

151 articles citing: The ProDom database of protein domain families: more emphasis on 3D

ContactPFP: Protein function prediction using predicted contact information. PMID:35875419
Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome. PMID:35784787
Innovative in Silico Approaches for Characterization of Genes and Proteins. PMID:35664302
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L. PMID:35328546
Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus. PMID:35022698
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. PMID:34585119
A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi). PMID:34249093
Evolution of networks of protein domain organization. PMID:34103558
AUTS2 Regulates RNA Metabolism and Dentate Gyrus Development in Mice. PMID:34013328
Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina. PMID:33604192
The Draft Genome Sequence of a New Land-Hopper Platorchestia hallaensis. PMID:33505439
Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). PMID:33441607
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity. PMID:33323129
The InterPro protein families and domains database: 20 years on. PMID:33156333
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. PMID:32817122
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. PMID:32514106
The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. PMID:32424221
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
A High-Quality Genome Sequence of Model Legume Lotus japonicus (MG-20) Provides Insights into the Evolution of Root Nodule Symbiosis. PMID:32365501
Sergentomyia schwetzi: Salivary gland transcriptome, proteome and enzymatic activities in two lineages adapted to different blood sources. PMID:32208452
First draft genome for the sand-hopper Trinorchestia longiramus. PMID:32152293
A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. PMID:32103005
Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation. PMID:31895412
Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1. PMID:31878043
A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. PMID:31685928
Draft Genome and Complete Hox-Cluster Characterization of the Sterlet (Acipenser ruthenus). PMID:31543900
Whole Genome Sequencing of Chinese White Dolphin (Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. PMID:31466310
Wheat wounding-responsive HD-Zip IV transcription factor GL7 is predominantly expressed in grain and activates genes encoding defensins. PMID:31183604
Comparative genomics sheds light on the predatory lifestyle of accipitrids and owls. PMID:30783131
Genome Assembly for a Yunnan-Guizhou Plateau "3E" Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications. PMID:30564274
Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales. PMID:30532075
Comparative genomics of downy mildews reveals potential adaptations to biotrophy. PMID:30486780
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
SDADB: a functional annotation database of protein structural domains. PMID:29961821
Computational Methods for Predicting Protein-Protein Interactions Using Various Protein Features. PMID:29927082
Transcriptional profiling of antioxidant defense system and heat shock protein (Hsp) families in the cadmium- and copper-exposed marine ciliate Euplotes crassu. PMID:29892903
BLAST-XYPlot Viewer: A Tool for Performing BLAST in Whole-Genome Sequenced Bacteria/Archaea and Visualize Whole Results Simultaneously. PMID:29789313
Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii. PMID:29659813
The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. PMID:29403466
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
Draft genome of the lined seahorse, Hippocampus erectus. PMID:28444302
Noumeavirus replication relies on a transient remote control of the host nucleus. PMID:28429720
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. PMID:28334975
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. PMID:28327943
Wheat drought-responsive WXPL transcription factors regulate cuticle biosynthesis genes. PMID:28161858
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
FlhF Is Required for Swarming Motility and Full Pathogenicity of Bacillus cereus. PMID:27807433
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions. PMID:27552220
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
Comparative Protein Structure Modeling Using MODELLER. PMID:27322406
Genome-scale prediction of moonlighting proteins using diverse protein association information. PMID:27153604
Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. PMID:26964738
BLAST-based structural annotation of protein residues using Protein Data Bank. PMID:26810894
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
The language of the protein universe. PMID:26451980
The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches. PMID:26380077
Constitutive overexpression of the TaNF-YB4 gene in transgenic wheat significantly improves grain yield. PMID:26220082
In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139. PMID:26175663
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PMID:26114425
Rv2031c of Mycobacterium tuberculosis: a master regulator of Rv2028-Rv2031 (HspX) operon. PMID:25964780
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
Genome-scale identification and characterization of moonlighting proteins. PMID:25497125
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
Computational characterization of moonlighting proteins. PMID:25399606
Text mining in cancer gene and pathway prioritization. PMID:25392685
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. PMID:25377941
A novel role for protein kinase Kin2 in regulating HAC1 mRNA translocation, splicing, and translation. PMID:25348718
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
Deciphering key features in protein structures with the new ENDscript server. PMID:24753421
Endosperm transfer cell-specific genes and proteins: structure, function and applications in biotechnology. PMID:24578704
Structure prediction of magnetosome-associated proteins. PMID:24523717
Finding the missing honey bee genes: lessons learned from a genome upgrade. PMID:24479613
InterProScan 5: genome-scale protein function classification. PMID:24451626
Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20. PMID:24391926
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. PMID:24302577
Minke whale genome and aquatic adaptation in cetaceans. PMID:24270359
Annotation extension through protein family annotation coherence metrics. PMID:24130572
Protein domain definition should allow for conditional disorder. PMID:23963781
Developmental gene discovery in a hemimetabolous insect: de novo assembly and annotation of a transcriptome for the cricket Gryllus bimaculatus. PMID:23671567
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. PMID:23651452
Role of Homeodomain leucine zipper (HD-Zip) IV transcription factors in plant development and plant protection from deleterious environmental factors. PMID:23584027
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. PMID:23514353
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. PMID:23180770
Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins. PMID:23173871
Dynamics of domain coverage of the protein sequence universe. PMID:23157439
XatA, an AT-1 autotransporter important for the virulence of Xylella fastidiosa Temecula1. PMID:22950010
MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses. PMID:22449399
Structure- and sequence-based function prediction for non-homologous proteins. PMID:22270458
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree. PMID:22121228
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
Sulfur metabolism in the extreme acidophile acidithiobacillus caldus. PMID:21687411
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. PMID:21472436
Identification and characterization of a bacterial glutamic peptidase. PMID:21122090
Computer aided selection of candidate vaccine antigens. PMID:21067543
Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, carbon fixation in A. ferrooxidans. PMID:20799944
Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immune-relevant genes in marine fish. PMID:20707909
More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PMID:20686689
Real-time ligand binding pocket database search using local surface descriptors. PMID:20455259
Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0. PMID:20178631
From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase. PMID:20043185
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. PMID:19923231
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. PMID:19910368
Visualising biological data: a semantic approach to tool and database integration. PMID:19534744
PSI-2: structural genomics to cover protein domain family space. PMID:19523904
Exploiting structural classifications for function prediction: towards a domain grammar for protein function. PMID:19398323
First gene cassettes of integrons as targets in finding adaptive genes in metagenomes. PMID:19363073
Protein function annotation by homology-based inference. PMID:19226439
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. PMID:19084081
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. PMID:19036790
Genome and proteome annotation: organization, interpretation and integration. PMID:19019817
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes. PMID:18984624
InterPro: the integrative protein signature database. PMID:18940856
Experience using web services for biological sequence analysis. PMID:18621748
Unraveling protein networks with power graph analysis. PMID:18617988
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. PMID:18613951
On the extent and origins of genic novelty in the phylum Nematoda. PMID:18596977
MACHOS: Markov clusters of homologous subsequences. PMID:18586748
Comparative protein structure modeling using Modeller. PMID:18428767
The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation. PMID:18221520
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
The Pfam protein families database. PMID:18039703
Improved human disease candidate gene prioritization using mouse phenotype. PMID:17939863
Troponin T isoform expression is modulated during Atlantic halibut metamorphosis. PMID:17577411
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. PMID:17547750
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. PMID:17425790
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PMID:17355171
Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. PMID:17254327
New developments in the InterPro database. PMID:17202162
Fine-tuning of protein domain boundary by minimizing potential coiled coil regions. PMID:17180444
A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells. PMID:17083467
Multiple alignment of protein sequences with repeats and rearrangements. PMID:17068081
Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. PMID:16872539
Analysis of bacteria-challenged wild silkmoth, Antheraea mylitta (lepidoptera) transcriptome reveals potential immune genes. PMID:16857061
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. PMID:16855290
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. PMID:16845116
A gold standard set of mechanistically diverse enzyme superfamilies. PMID:16507141
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. PMID:16481312
YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. PMID:16385049
Phytome: a platform for plant comparative genomics. PMID:16381967
VMD: a community annotation database for oomycetes and microbial genomes. PMID:16381891
An examination of dynamics crosstalk between SH2 and SH3 domains by hydrogen/deuterium exchange and mass spectrometry. PMID:16322569
JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture. PMID:16135248
Bioinformatics in microbial biotechnology--a mini review. PMID:15985162
InterProScan: protein domains identifier. PMID:15980438
Databases and information integration for the Medicago truncatula genome and transcriptome. PMID:15888676
ProDom: automated clustering of homologous domains PubMed citations: 137.

137 articles citing: ProDom: automated clustering of homologous domains

The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis. PMID:35733792
A novel gene from the acidophilic bacterium Leptospirillum sp. CF-1 and its role in oxidative stress and chromate tolerance. PMID:35525996
The genome of medicinal leech (Whitmania pigra) and comparative genomic study for exploration of bioactive ingredients. PMID:35073842
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae. PMID:34659355
Classification of protein domains based on their three-dimensional shapes (CPD3DS). PMID:34541344
Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato. PMID:34451581
Draft Genome of the Mirrorwing Flyingfish (Hirundichthys speculiger). PMID:34306036
Draft genome of a biparental beetle species, Lethrus apterus. PMID:33902445
The Draft Genome of Red Lechwe, Kobus leche leche. PMID:33250921
How Tupanvirus Degrades the Ribosomal RNA of Its Amoebal Host? The Ribonuclease T2 Track. PMID:32849355
A draft genome assembly of spotted hyena, Crocuta crocuta. PMID:32345970
Computational Analysis of the Hypothetical Protein P9303_05031 from Marine Cyanobacterium Prochlorococcus Marinus MIT 9303. PMID:32229666
Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study. PMID:32108239
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Draft Genome of the Asian Buffalo Leech Hirudinaria manillensis. PMID:32010187
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
DeepDom: Predicting protein domain boundary from sequence alone using stacked bidirectional LSTM. PMID:30864311
Genome structure and evolution of Antirrhinum majus L. PMID:30692677
Identification of a perchloric acid-soluble protein (PSP)-like ribonuclease from Trichomonas vaginalis. PMID:30191309
Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger. PMID:29375499
Improving pairwise comparison of protein sequences with domain co-occurrence. PMID:29293498
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp. PMID:28172869
Protein Bioinformatics Databases and Resources. PMID:28150231
The Streptococcus gordonii Adhesin CshA Protein Binds Host Fibronectin via a Catch-Clamp Mechanism. PMID:27920201
An Alkaline Protease from Bacillus pumilus MP 27: Functional Analysis of Its Binding Model toward Its Applications As Detergent Additive. PMID:27536284
Comparative Genomics of the Sigatoka Disease Complex on Banana Suggests a Link between Parallel Evolutionary Changes in Pseudocercospora fijiensis and Pseudocercospora eumusae and Increased Virulence on the Banana Host. PMID:27513322
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences. PMID:27307636
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA. PMID:26581084
Cloning, expression, characterization and mutational analysis of the tfdA gene from Cupriavidus campinensis BJ71. PMID:25850533
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PMID:25330359
Conserved C-terminal nascent peptide binding domain of HYPK facilitates its chaperone-like activity. PMID:25116620
SCEDS: protein fragments for molecular replacement in Phaser. PMID:24189233
Mediation of clathrin-dependent trafficking during cytokinesis and cell expansion by Arabidopsis stomatal cytokinesis defective proteins. PMID:24179130
ThreaDom: extracting protein domain boundary information from multiple threading alignments. PMID:23812990
The signatures of selection for translational accuracy in plant genes. PMID:23695187
Thiol/Disulfide system plays a crucial role in redox protection in the acidophilic iron-oxidizing bacterium Leptospirillum ferriphilum. PMID:22970253
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. PMID:22942020
Computational analysis of the ESX-1 region of Mycobacterium tuberculosis: insights into the mechanism of type VII secretion system. PMID:22140496
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes. PMID:22139920
CastorDB: a comprehensive knowledge base for Ricinus communis. PMID:21914200
Molecular evolution of the LNX gene family. PMID:21827680
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
Characterization of Lovastatin biosynthetic cluster proteins in Aspergillus terreus strain ATCC 20542. PMID:21738324
Ortholog identification in the presence of domain architecture rearrangement. PMID:21712343
Macromolecular assembly of polycystin-2 intracytosolic C-terminal domain. PMID:21622852
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus. PMID:21569391
Genetic and epigenetic association studies suggest a role of microRNA biogenesis gene exportin-5 (XPO5) in breast tumorigenesis. PMID:21552306
Ultra-fast sequence clustering from similarity networks with SiLiX. PMID:21513511
The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases. PMID:21498547
A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PMID:21455299
Structural basis of Streptococcus pyogenes immunity to its NAD+ glycohydrolase toxin. PMID:21300288
The Mycobacterium tuberculosis high-affinity iron importer, IrtA, contains an FAD-binding domain. PMID:19948799
GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes. PMID:19917126
A survey of integral alpha-helical membrane proteins. PMID:19760129
Structural and functional constraints in the evolution of protein families. PMID:19756040
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. PMID:19717629
MrdH, a novel metal resistance determinant of Pseudomonas putida KT2440, is flanked by metal-inducible mobile genetic elements. PMID:19648243
Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus. PMID:19604367
Interaction of actin and the chloroplast protein import apparatus. PMID:19435889
Analyses of domains and domain fusions in human proto-oncogenes. PMID:19292927
Cloning and characterization of two novel crystal protein genes, cry54Aa1 and cry30Fa1, from Bacillus thuringiensis strain BtMC28. PMID:19280260
Domain mobility in proteins: functional and evolutionary implications. PMID:19151098
Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations. PMID:19055775
D-Glucose sensing by a plasma membrane regulator of G signaling protein, AtRGS1. PMID:18817773
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. PMID:18782832
Powerful fusion: PSI-BLAST and consensus sequences. PMID:18678588
On the extent and origins of genic novelty in the phylum Nematoda. PMID:18596977
MACHOS: Markov clusters of homologous subsequences. PMID:18586748
Wdnm1-like, a new adipokine with a role in MMP-2 activation. PMID:18492766
Empirical comparison of ab initio repeat finding programs. PMID:18287116
Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins. PMID:17663785
Identification of sensory and signal-transducing domains in two-component signaling systems. PMID:17628134
Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii. PMID:17400776
Acheron, a novel member of the Lupus Antigen family, is induced during the programmed cell death of skeletal muscles in the moth Manduca sexta. PMID:17383118
Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments. PMID:17369271
Cloning and characterization of a novel crystal protein from a native Bacillus thuringiensis isolate highly active against Aedes aegypti. PMID:17334846
False occurrences of functional motifs in protein sequences highlight evolutionary constraints. PMID:17331242
Helicobacter pylori EstV: identification, cloning, and characterization of the first lipase isolated from an epsilon-proteobacterium. PMID:17293528
Expanded protein information at SGD: new pages and proteome browser. PMID:17142221
EVEREST: a collection of evolutionary conserved protein domains. PMID:17099230
Ala394Thr polymorphism in the clock gene NPAS2: a circadian modifier for the risk of non-Hodgkin's lymphoma. PMID:17096334
Tracing the origin of functional and conserved domains in the human proteome: implications for protein evolution at the modular level. PMID:17090320
A peptidoglycan hydrolase motif within the mycobacteriophage TM4 tape measure protein promotes efficient infection of stationary phase cells. PMID:17083467
Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. PMID:17065317
Maintenance DNA methyltransferase (Met1) and silencing of CpG-methylated foreign DNA in Volvox carteri. PMID:17033890
Formation of the Arabidopsis pentatricopeptide repeat family. PMID:16825340
A limited universe of membrane protein families and folds. PMID:16815920
EVEREST: automatic identification and classification of protein domains in all protein sequences. PMID:16749920
Refining multiple sequence alignments with conserved core regions. PMID:16707662
Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions. PMID:16602695
NovelFam3000--uncharacterized human protein domains conserved across model organisms. PMID:16533400
The U-box protein CMPG1 is required for efficient activation of defense mechanisms triggered by multiple resistance genes in tobacco and tomato. PMID:16531490
Phytome: a platform for plant comparative genomics. PMID:16381967
INVHOGEN: a database of homologous invertebrate genes. PMID:16381884
The riddle of the plant vacuolar sorting receptors. PMID:16333569
The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. PMID:16126837
The MicrobesOnline Web site for comparative genomics. PMID:15998914
Distribution of immunodeficiency fact files with XML--from Web to WAP. PMID:15978138
Solution structure of the helicase-interaction domain of the primase DnaG: a model for helicase activation. PMID:15837199
Comparative mapping of sequence-based and structure-based protein domains. PMID:15790427
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. PMID:15784138
BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools. PMID:15757512
Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target. PMID:15704012
New strategy for identification of novel Cry-type genes from Bacillus thuringiensis strains. PMID:15691928
Identification of three critical acidic residues of poly(ADP-ribose) glycohydrolase involved in catalysis: determining the PARG catalytic domain. PMID:15658938
The path to enlightenment: making sense of genomic and proteomic information. PMID:15629052
The ProDom database of protein domain families: more emphasis on 3D. PMID:15608179
InterPro, progress and status in 2005. PMID:15608177
ADDA: a domain database with global coverage of the protein universe. PMID:15608174
The Universal Protein Resource (UniProt). PMID:15608167
Expression screening, protein purification and NMR analysis of human protein domains for structural genomics. PMID:15263851
Sequence-based prediction of protein domains. PMID:15240828
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. PMID:15215441
Interaction profile-based protein classification of death domain. PMID:15189571
Visualizing sequence similarity of protein families. PMID:15140831
Progress towards mapping the universe of protein folds. PMID:15128436
A hybrid clustering approach to recognition of protein families in 114 microbial genomes. PMID:15115543
Identification of differentially expressed cDNA sequences in ovaries of sexual and apomictic plants of Brachiaria brizantha. PMID:15082923
The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer. PMID:15040816
Comparative analysis of protein domain organization. PMID:14993202
A description of the Mei2-like protein family; structure, phylogenetic distribution and biological context. PMID:14986133
PHYTOPROT: a database of clusters of plant proteins. PMID:14681432
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites. PMID:14681425
MODBASE, a database of annotated comparative protein structure models, and associated resources. PMID:14681398
UniProt: the Universal Protein knowledgebase. PMID:14681372
Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis. PMID:14675496
Enzyme-specific profiles for genome annotation: PRIAM. PMID:14602924
Structural genomics: computational methods for structure analysis. PMID:12930981
Target selection and determination of function in structural genomics. PMID:12880206
Three monophyletic superfamilies account for the majority of the known glycosyltransferases. PMID:12824488
GlobPlot: Exploring protein sequences for globularity and disorder. PMID:12824398
Tools for comparative protein structure modeling and analysis. PMID:12824331
ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. PMID:12824317
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. PMID:12520029
http://dx.doi.org/10.1093/nar/28.1.267

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classification
metasource: Fairsharing.org
version: FAIRsharing.org: ProDom; ProDom; DOI: https://doi.org/10.25504/FAIRsharing.a8z6gz; Last edited: April 26, 2021, 9:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: ProDom; ProDom; DOI: https://doi.org/10.25504/FAIRsharing.a8z6gz; Last edited: April 26, 2021, 9:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: ProDom; ProDom; DOI: https://doi.org/10.25504/FAIRsharing.a8z6gz; Last edited: April 26, 2021, 9:33 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556

protein folds and structural domains
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:13.516556

classification protein protein domain protein sequence protein domains and classification gene and protein families protein folds and structural domains

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ADDA - A Domain Database

FunShift

InterDom

Conserved Domain Database

Pfam

Simple Modular Architecture Research Tool

EVEREST - EVolutionary Ensembles of REcurrent SegmenTs

iPfam

Integrated resource of protein families, domains and functional sites

SBASE

SUPFAM

DomIns - Database of Domain Insertions

SUPERFAMILY

LenVarDB

Protein Clusters

ProtoNet

PROSITE

PALI

SCOPe

NRichD