Institute of Biochemistry

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11 to 20 of 1,351 Results

SAM.xml Apr 28, 2025 - MD Simulations with PRDM9 XML - 20.9 KB - MD5: 8504b192cebc39de3edb5595d94cd0e4 Parameter file for cofactor SAM
ZNB.xml Apr 28, 2025 - MD Simulations with PRDM9 XML - 1.6 KB - MD5: a8f183de30b9a05bd6a6515d639ea88c Parameter file for zinc ions
NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases" Jan 13, 2025 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel, 2025, "NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"", https://doi.org/10.18419/DARUS-4515, DaRUS, V1, UNF:6:bSvQoJxvb+T/iyQGPOvTBA== [fileUNF] Analysis of flanking sequence preference with a randomized substrate and bioinformatic data For analysis of the flanking sequence preference, substrate with different target sites sites in a 9 or 10 bp randomized sequence context were prepared as described (Dukatz, et al. 2020; Dukatz, et al. 2022). Substrate methylation reactions were performed wi...
raw_data.zip Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases" ZIP Archive - 177.1 MB - MD5: 6e0120fb5866aaffd82db1fbfa76b252
readme-1.pdf Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases" Adobe PDF - 104.6 KB - MD5: 1fa8ecab0ba68b617138a98d90160ffc Description of the data structure
source_data.xlsx Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases" MS Excel Spreadsheet - 736.2 KB - MD5: ddd9a622dbb5638621ca557e01fc4ec2
Supplementary_Table_S1.tab Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases" Tabular Data - 53.3 KB - 8 Variables, 1106 Observations - UNF:6:bSvQoJxvb+T/iyQGPOvTBA== Assignment of experiments and data files and overview of the number of reads in CSV format
Supplementary Table S1.xlsx Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases" MS Excel Spreadsheet - 56.4 KB - MD5: a3df4453d1eb9612fabd87027482cfbe Assignment of experiments and data files and overview of the number of reads
Data related to Panzer: A Machine Learning Based Approach to Analyze Supersecondary Structures of Proteins Nov 27, 2024 Panzer, Tim, 2024, "Data related to Panzer: A Machine Learning Based Approach to Analyze Supersecondary Structures of Proteins", https://doi.org/10.18419/DARUS-4576, DaRUS, V1 This entry contains the data used to implement the bachelor thesis. It was investigated how embeddings can be used to analyze supersecondary structures. Abstract of the thesis: This thesis analyzes the behavior of supersecondary structures in the context of embeddings. For this purpose, data from the Protein Topology Graph Library was provided with...
1_data_retrival.ipynb Nov 27, 2024 - Data related to Panzer: A Machine Learning Based Approach to Analyze Supersecondary Structures of Proteins Jupyter Notebook - 3.5 KB - MD5: 5aed17f7e8f45b9c585d0fdfc2d3abe1

SAM.xml

Apr 28, 2025 - MD Simulations with PRDM9

XML - 20.9 KB -

Parameter file for cofactor SAM

ZNB.xml

Apr 28, 2025 - MD Simulations with PRDM9

XML - 1.6 KB -

Parameter file for zinc ions

NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"

Jan 13, 2025 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel, 2025, "NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"", https://doi.org/10.18419/DARUS-4515, DaRUS, V1, UNF:6:bSvQoJxvb+T/iyQGPOvTBA== [fileUNF]

Analysis of flanking sequence preference with a randomized substrate and bioinformatic data For analysis of the flanking sequence preference, substrate with different target sites sites in a 9 or 10 bp randomized sequence context were prepared as described (Dukatz, et al. 2020; Dukatz, et al. 2022). Substrate methylation reactions were performed wi...

raw_data.zip

Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"

ZIP Archive - 177.1 MB -

readme-1.pdf

Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"

Adobe PDF - 104.6 KB -

Description of the data structure

source_data.xlsx

Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"

MS Excel Spreadsheet - 736.2 KB -

Supplementary_Table_S1.tab

Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"

Tabular Data - 53.3 KB - 8 Variables, 1106 Observations -

Assignment of experiments and data files and overview of the number of reads in CSV format

Supplementary Table S1.xlsx

Jan 13, 2025 - NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"

MS Excel Spreadsheet - 56.4 KB -

Assignment of experiments and data files and overview of the number of reads

Data related to Panzer: A Machine Learning Based Approach to Analyze Supersecondary Structures of Proteins

Nov 27, 2024

Panzer, Tim, 2024, "Data related to Panzer: A Machine Learning Based Approach to Analyze Supersecondary Structures of Proteins", https://doi.org/10.18419/DARUS-4576, DaRUS, V1

This entry contains the data used to implement the bachelor thesis. It was investigated how embeddings can be used to analyze supersecondary structures. Abstract of the thesis: This thesis analyzes the behavior of supersecondary structures in the context of embeddings. For this purpose, data from the Protein Topology Graph Library was provided with...

1_data_retrival.ipynb

Nov 27, 2024 - Data related to Panzer: A Machine Learning Based Approach to Analyze Supersecondary Structures of Proteins

Jupyter Notebook - 3.5 KB -

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