Contact and support
Need help, have a question, or want to contact the ResearchHub team?
© 2026 ResearchHub. Built for responsible scholarly connection.
Privacy-aware community infrastructureResearch graph
References from In silico discovery of selenocysteine-containing variants of Group 4 [NiFe] hydrogenases. Local targets link to admitted publications; unresolved targets remain external evidence.
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
Nickel–iron–selenium hydrogenases – an overview
10.1002/ejic.201001127 · 2011 · External reference
The energy-converting hydrogenase Ech2 is important for the growth of the thermophilic acetogen Thermoanaerobacter kivui on ferredoxin-dependent substrates
10.1128/spectrum.03380-23 · 2024 · External reference
Sensitive protein alignments at tree-of-life scale using DIAMOND
10.1038/s41592-021-01101-x · 2021 · External reference
Clustering the protein universe of life using DIAMOND DeepClust
10.1038/s41592-026-03030-z · 2026 · External reference
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
10.1093/bioinformatics/btp348 · 2009 · External reference
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
10.1093/nar/gkab688 · 2021 · External reference
GTDB-Tk v2: memory friendly classification with the genome taxonomy database
10.1093/bioinformatics/btac672 · 2022 · External reference
OrthoFinder: phylogenetic orthology inference for comparative genomics
10.1186/s13059-019-1832-y · 2019 · External reference
Selective cysteine-to-selenocysteine changes in a [NiFe]-hydrogenase confirm a special position for catalysis and oxygen tolerance
10.1073/pnas.2100921118 · 2021 · External reference
Replacing a cysteine ligand by selenocysteine in a [NiFe]-hydrogenase unlocks hydrogen production activity and addresses the role of concerted proton-coupled electron transfer in electrocatalytic reversibility
10.1021/jacs.4c03489 · 2024 · External reference
Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases
10.1021/cr050195z · 2007 · External reference
Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein
10.1038/342453a0 · 1989 · External reference
Thermodesulfobium acidiphilum sp. nov., a thermoacidophilic, sulfate-reducing, chemoautotrophic bacterium from a thermal site
10.1099/ijsem.0.001745 · 2017 · External reference
COG database update 2024
10.1093/nar/gkae983 · 2025 · External reference
The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center
10.1016/s0969-2126(99)80072-0 · 1999 · External reference
Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival
10.1038/ismej.2015.153 · 2016 · External reference
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
10.1093/sysbio/syq010 · 2010 · External reference
The molybdenum active site of formate dehydrogenase is capable of catalyzing C–H bond cleavage and oxygen atom transfer reactions
10.1021/acs.biochem.6b00002 · 2016 · External reference
Simulated early Earth geochemistry fuels a hydrogen-dependent primordial metabolism
10.1038/s41559-025-02676-w · 2025 · External reference
UFBoot2: improving the ultrafast bootstrap approximation
10.1093/molbev/msx281 · 2018 · External reference
SECIS element variability and its role in selenocysteine versus cysteine utilization in SelD enzymes
10.11299/metallomicsresearch.mr202408 · 2024 · External reference
The hyp operon gene products are required for the maturation of catalytically active hydrogenase isoenzymes in Escherichia coli
10.1007/bf00276307 · 1992 · External reference
ModelFinder: fast model selection for accurate phylogenetic estimates
10.1038/nmeth.4285 · 2017 · External reference
MAFFT multiple sequence alignment software version 7: improvements in performance and usability
10.1093/molbev/mst010 · 2013 · External reference
Hydrogenases for biological hydrogen production
10.1016/j.biortech.2011.02.113 · 2011 · External reference
Genetic probing of the interaction between the translation factor SelB and its mRNA binding element in Escherichia coli
10.1007/s004380051143 · 1999 · External reference
Biological hydrogen production: prospects and challenges
10.1016/j.tibtech.2010.01.007 · 2010 · External reference
Gene for a novel tRNA species that accepts l-serine and cotranslationally inserts selenocysteine
10.1038/331723a0 · 1988 · External reference
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool
10.1093/nar/gkae268 · 2024 · External reference
Hydrogenases
10.1021/cr4005814 · 2014 · External reference
Heterotrophic lifestyle in the phylum Thermodesulfobiota revealed by physiological and genomic characterization of the acidophilic sulfate-reducing bacterium Thermodesulfobium fumaratoxidans sp. nov
10.1016/j.syapm.2025.126684 · 2026 · External reference
The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis
10.1038/nchembio.2335 · 2017 · External reference
Bacterial formate hydrogenlyase complex
10.1073/pnas.1407927111 · 2014 · External reference
A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring
10.1007/s00792-003-0320-0 · 2003 · External reference
The difference a Se makes? Oxygen-tolerant hydrogen production by the [NiFeSe]-hydrogenase from Desulfomicrobium baculatum
10.1021/ja803657d · 2008 · External reference
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
10.1093/nar/gkab776 · 2022 · External reference
[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation
10.1016/j.bbamcr.2014.11.021 · 2015 · External reference
FastTree 2 – approximately maximum-likelihood trees for large alignments
10.1371/journal.pone.0009490 · 2010 · External reference
RNA secondary structure prediction using deep learning with thermodynamic integration
10.1038/s41467-021-21194-4 · 2021 · External reference
Database resources of the National Center for Biotechnology Information in 2026
10.1093/nar/gkaf1060 · 2026 · External reference
Energy conservation by a hydrogenase-dependent chemiosmotic mechanism in an ancient metabolic pathway
10.1073/pnas.1818580116 · 2019 · External reference
Complex multimeric [FeFe] hydrogenases: biochemistry, physiology and new opportunities for the hydrogen economy
10.3389/fmicb.2018.02911 · 2018 · External reference
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
10.1371/journal.pone.0163962 · 2016 · External reference
HydDB: a web tool for hydrogenase classification and analysis
10.1038/srep34212 · 2016 · External reference
Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli
10.1038/s41467-022-32831-x · 2022 · External reference
Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNACys and elongation factor SelB
10.1080/15476286.2018.1474074 · 2018 · External reference
Occurrence, classification, and biological function of hydrogenases: an overview
10.1021/cr050196r · 2007 · External reference
Crystal structure of the nickel–iron hydrogenase from Desulfovibrio gigas
10.1038/373580a0 · 1995 · External reference
The conserved domain database in 2023
10.1093/nar/gkac1096 · 2023 · External reference
IQ-TREE 3: phylogenomic inference software using complex evolutionary models
10.1093/molbev/msag117 · 2026 · External reference
Structural insights into the biotechnologically relevant reversible NADPH-oxidizing NiFe-hydrogenase from P. furiosus
10.1016/j.str.2025.05.017 · 2025 · External reference
Structure of an ancient respiratory system
10.1016/j.cell.2018.03.071 · 2018 · External reference
An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes
10.1093/bioinformatics/bti400 · 2005 · External reference
Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues
10.1186/gb-2006-7-10-r94 · 2006 · External reference
Recent advances in exploring the composition and evolution of the prokaryotic selenoproteome
10.1128/aem.00556-26 · 2026 · External reference
Cotranslational insertion of selenocysteine into formate dehydrogenase from Escherichia coli directed by a UGA codon
10.1073/pnas.84.10.3156 · 1987 · External reference
Features of the formate dehydrogenase mRNA necessary for decoding of the UGA codon as selenocysteine
10.1073/pnas.87.12.4660 · 1990 · External reference
