51 to 60 of 70 Results
Jun 1, 2020 - Glycoside Hydrolase 19 Engineering Database
Orlando, Marco, 2020, "Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database", https://doi.org/10.18419/DARUS-803, DaRUS, V1
A starting alignment was built if other sequences with a known PDB structure were available, by performing a GH19 domain structure-based alignment generated through the mmaker command implemented in ChimeraX. Other seed sequences in the same superfamily were added to this fixed structural alignment by the use of “--add” flag option available in MAF... |
Jun 1, 2020 - Glycoside Hydrolase 19 Engineering Database
Orlando, Marco, 2020, "Seed sequences for the Glycoside Hydrolase 19 Engineering Database", https://doi.org/10.18419/DARUS-804, DaRUS, V1
Query sequences for the individual BLAST searches used to initialize the Glycoside Hydrolase 19 Engineering Database (GH19ED, https://gh19ed.biocatnet.de/). |
Jun 1, 2020 - Glycoside Hydrolase 19 Engineering Database
Orlando, Marco, 2020, "GraphML files for protein sequence networks of glycoside hydrolase 19 homologues", https://doi.org/10.18419/DARUS-802, DaRUS, V1
GraphML files for undirected weighted graphs with nodes that represent protein sequences of glycoside hydrolase 19 homologues. Protein sequences were clustered by a threshold of 90% sequence identity to derive representative sequences. Pairwise sequence identity between two sequences was derived from global Needleman-Wunsch alignment. Protein seque... |
May 18, 2020Bioinformatics
Supporting information and original files for bioinformatic investigations using the Glycoside Hydrolase 19 Engineering Database (https://gh19ed.biocatnet.de/) |
Apr 9, 2020 - Expansin Engineering Database
Lohoff, Caroline, 2020, "Conserved positions in expansin homologues", https://doi.org/10.18419/DARUS-735, DaRUS, V1, UNF:6:HemykMznkJ0tyrf89mswkg== [fileUNF]
Conserved positions in the N- and C-terminal expansin domains of different groups from the Expansin Engineering Database (occurring in at least 70% of the annotated sequence entries). The expansin domains were annotated using hmmscan (from the HMMER software suite) against all sequence entries in the Expansin Engineering Database. |
Apr 9, 2020 - Expansin Engineering Database
Buchholz, Patrick C. F., 2020, "Expansin homologues in actinobacterial genomes from South Africa", https://doi.org/10.18419/DARUS-699, DaRUS, V1
Hit sequences for putative expansins (or expansin domains) are reported from an exemplary genome screening. Five actinobacterial genomes were selected to show the application of the Expansin Engineering Database (ExED) for the identification of expansin domains. The original nucleic acid sequences were translated by the standard codon usage table i... |
Apr 9, 2020 - Expansin Engineering Database
Lohoff, Caroline, 2020, "Occurrence of expansins in the tree of life", https://doi.org/10.18419/DARUS-693, DaRUS, V1, UNF:6:eK0oQia4QiaiEO0m1BJFeA== [fileUNF]
Comparison between expansins found in the Expansin Engineering Database (ExED) and literature. |
Apr 2, 2020Bioinformatics
Supporting information and original files for bioinformatic investigations using the Expansin Engineering Database (https://exed.biocatnet.de/) |
Jeltsch, Albert; Bashtrykov, Pavel; Emperle, Max; Adam, Sabrina; Dukatz, Michael, 2020, "Deep enzymology data related to Gao et al.: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms", https://doi.org/10.18419/DARUS-627, DaRUS, V1
Experimental procedures: Libraries of double stranded DNA substrates with CpG, CpH or CpN sites in randomized sequence context were methlyated by DNMT3A or DNMT3B. Reactions were stopped by shock freezing in liquid nitrogen, then treated with proteinase K for 2 hours. Afterwards, the DNA was digested with the BsaI-HFv2 enzyme and a hairpin was liga... |
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2020, "Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation", https://doi.org/10.18419/DARUS-629, DaRUS, V1
Methylation of long hemimethylated DNA substrates: Methylation of the 349 bp long hemimethylated substrate with DNMT1 was carried out in 1X methylation buffer (100 mM HEPES, 1 mM EDTA, 0.5 mM DTT, 0.1 mg/mL BSA, pH 7.2 with KOH) in the presence of 1 mM AdoMet. For the methylation reactions, mixtures containing different DNMT1 concentrations were pr... |
