31 to 40 of 60 Results
Feb 15, 2022 - EnzymeML at work
Lagerman, Colton, 2022, "Synthesis and Hydrolysis of Cephalexin", https://doi.org/10.18419/DARUS-2468, DaRUS, V1
Investigated was the synthesis and hydrolysis of cephalexin, and the hydrolysis of phenylglycine methyl ester by an amino ester hydrolase. The concentrations of all reactants over time were measured, for four different initial concentrations of cephalexin and phenylglycine methyl ester. For each of the reactants, 9 data points are given over a time... |
Feb 15, 2022 - EnzymeML at work
Ngubane, Sandile, 2022, "Oxidation of ABTS by Trametes versicolor laccase", https://doi.org/10.18419/DARUS-2467, DaRUS, V1
Investigated was the oxidation of ABTS and syringaldazine by Trametes versicolor laccase. For this, the concentration of the substrate over time was measured, for different initial concentrations. All measurements were repeated for three replicates. |
Feb 15, 2022 - EnzymeML at work
Spöring, Jan-Dirk, 2022, "Propioin Synthesis using Benzoin Aldolase", https://doi.org/10.18419/DARUS-2466, DaRUS, V1
Investigated was the ligation of two molecules propanal in organic conditions, catalysed by the benzoin aldolase, which was added in the form of lyophillised whole cells. The reaction was performed in triplicate, with 200 mM as the starting concentration of the propanal in all cases. Triethanolamine was chosen as buffer, together with Cyclopentyl m... |
Feb 1, 2022 - MD Simulations
Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen, 2022, "Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/DARUS-2463, DaRUS, V1
Python scripts used for the Molecular Dynamics Simulation presented in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects" |
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2021, "Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns", https://doi.org/10.18419/DARUS-2114, DaRUS, V2
Experimental procedures for deep enzymology reactions with randomized substrates: For analysis of flanking sequence preferences of the TET enzymes, a similar approach as described for DNMTs (Emperle et al., 2019; Gao et al., 2020; Adam et al., 2020; Dukatz et al., 2020) was used. Briefly, the following single-stranded oligonucleotides containing a... |
Dec 1, 2021 - Plastics-Active Enzymes Database
Buchholz, Patrick C. F., 2021, "GraphML files for sequence networks of PETases and PURases", https://doi.org/10.18419/DARUS-2054, DaRUS, V1
The GraphML files contain the sequence networks and annotated metadata for protein sequences. |
Dec 1, 2021 - Plastics-Active Enzymes Database
Buchholz, Patrick C. F., 2021, "Profile hidden Markov model for PETase homologues", https://doi.org/10.18419/DARUS-2055, DaRUS, V1, UNF:6:AEjnqfOrnimO5Q2xFDkQDw== [fileUNF]
Sixteen protein sequences for enzymes with known activity against polyethylene terephthalate (PET) were clustered using CD-HIT to derive a reduced set of twelve centroid sequences. These twelve protein sequences were aligned in a structure-guided multiple sequence alignment by T-COFFEE. A profile hidden Markov model (HMM) was derived from this mult... |
Nov 25, 2021 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Bröhm, Alexander; Dukatz, Michael; Adam, Sabrina, 2021, "NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3", https://doi.org/10.18419/DARUS-1252, DaRUS, V2
Methylation experiments: For the competitive nucleosome methylation experiments, 0.6 pmol of each nucleosome variant were digested with MluI (NEB) for 60 min at 37°C in 10 µL NEB Cutsmart buffer (50 mM KOAc/20 mM Tris-acetate pH 7.9, 10 mM Magnesium Acetate, 100 µg/mL BSA) to remove residual unbound DNA. Afterwards, DNMT3A2 or DNMT3AC was added to... |
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Mack, Alexandra; Emperle, Max, 2021, "Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/DARUS-2231, DaRUS, V1
Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with a distance of 12 base pairs between CpG sites were obtained from IDT. Second strand synthesis was conducted by a primer extension reaction using one universal primer. The obtained library of double-stranded DNA oligonucleot... |
May 20, 2021 - Glycoside Hydrolase 19 Engineering Database
Buchholz, Patrick C. F., 2021, "Sequence cross-references and taxonomic lineage for glycoside hydrolase family 19", https://doi.org/10.18419/DARUS-1163, DaRUS, V1, UNF:6:zi8TRxkq1C/pCN14pXTA0Q== [fileUNF]
The Glycoside Hydrolase 19 Engineering Database (GH19ED) contains information on protein sequences and structures of glycoside hydrolases from family 19. This dataset lists cross-references to the National Center for Biotechnology Information (NCBI), cross-references to the Protein Data Bank (PDB) and the taxonomic lineage for each sequence entry i... |
