Institute of Biochemistry

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1,061 to 1,070 of 1,362 Results

Enspara_Clustering_Analysis.py Mar 2, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide Plain Text - 1.4 KB - MD5: 52c57eb9028afc94ccc2504c680e1ef6 Python script to analyse the output of the enspara output files (generated with "Enspara_Command.txt")
Enspara_Command.txt Mar 2, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide Plain Text - 642 B - MD5: 25782c1c72742bed83986eab713de328 Command line input for the enspara python library. Needs follow up from "Enspara_Clustering_Analysis.py".
Production_Peptide_in_solution.py Mar 2, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide Plain Text - 7.2 KB - MD5: c647bc59527d69986f4c89f3da39669d Python script for the production of peptide in solution MD simulation trajectories.
Production_SETD2-peptide-complex.py Mar 2, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide Plain Text - 13.5 KB - MD5: d90ac856931817507afa24516f17142c Python script for the production of enzyme-peptide complex MD simulation trajectories.
Production_SETD2_sMD.py Mar 2, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide Plain Text - 17.5 KB - MD5: 475202d1a38ec4bbdae9527e1514024b Python script for the production of peptide-enzyme association sMD simulation trajectories.
README.pdf Mar 2, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide Adobe PDF - 147.5 KB - MD5: 8f97c7be1d9767736e3b5cae7157c9be Description of the python scripts provided in this repository. Instructions for use, installation and outcome.
Catalysis of L-cysteine by IscS in the presence of IscU Feb 15, 2022 - EnzymeML at work Pinto, Maria Filipa, 2022, "Catalysis of L-cysteine by IscS in the presence of IscU", https://doi.org/10.18419/DARUS-2483, DaRUS, V1 Measured was the reaction from cysteine to alanine by the Cysteine desulfurase, for six different initial concentrations of cysteine. The data consists of three data points over the course of 2.5 minutes for alanine. Additionally, the concentration of cysteine over time was calculated from the given values, for the later modelling.
AnalysingInitialRateDataUsingMichaelisMentenKineticsinterferENZY.ipynb Feb 15, 2022 - Catalysis of L-cysteine by IscS in the presence of IscU Jupyter Notebook - 48.9 KB - MD5: f35f461622c4204a4e279458bccd14ce Used to generate an InterferEnzy file from an OMEX EnzymeML archive, which was the sent to the modeling platform to estimate the parameters.
AnalysingInitialRateDataUsingMichaelisMentenKineticsJupyterNotebook.ipynb Feb 15, 2022 - Catalysis of L-cysteine by IscS in the presence of IscU Jupyter Notebook - 55.2 KB - MD5: 12615450c9a703b35f21a3e9af6f2a4f Used to model the given OMEX EnzymeML archive using the Python package lmfit.
Desulfuration_Cysteine_Pinto_input_interferENZY.txt Feb 15, 2022 - Catalysis of L-cysteine by IscS in the presence of IscU Plain Text - 370 B - MD5: 679c41f97de6f72684385e95865cb715 Text file that is used as input for InterferEnzy

Enspara_Clustering_Analysis.py

Mar 2, 2022 - Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide

Plain Text - 1.4 KB -

Python script to analyse the output of the enspara output files (generated with "Enspara_Command.txt")

Enspara_Command.txt

Plain Text - 642 B -

Command line input for the enspara python library. Needs follow up from "Enspara_Clustering_Analysis.py".

Production_Peptide_in_solution.py

Plain Text - 7.2 KB -

Python script for the production of peptide in solution MD simulation trajectories.

Production_SETD2-peptide-complex.py

Plain Text - 13.5 KB -

Python script for the production of enzyme-peptide complex MD simulation trajectories.

Production_SETD2_sMD.py

Plain Text - 17.5 KB -

Python script for the production of peptide-enzyme association sMD simulation trajectories.

README.pdf

Adobe PDF - 147.5 KB -

Description of the python scripts provided in this repository. Instructions for use, installation and outcome.

Catalysis of L-cysteine by IscS in the presence of IscU

Feb 15, 2022 - EnzymeML at work

Pinto, Maria Filipa, 2022, "Catalysis of L-cysteine by IscS in the presence of IscU", https://doi.org/10.18419/DARUS-2483, DaRUS, V1

Measured was the reaction from cysteine to alanine by the Cysteine desulfurase, for six different initial concentrations of cysteine. The data consists of three data points over the course of 2.5 minutes for alanine. Additionally, the concentration of cysteine over time was calculated from the given values, for the later modelling.

AnalysingInitialRateDataUsingMichaelisMentenKineticsinterferENZY.ipynb

Feb 15, 2022 - Catalysis of L-cysteine by IscS in the presence of IscU

Jupyter Notebook - 48.9 KB -

Used to generate an InterferEnzy file from an OMEX EnzymeML archive, which was the sent to the modeling platform to estimate the parameters.

AnalysingInitialRateDataUsingMichaelisMentenKineticsJupyterNotebook.ipynb

Feb 15, 2022 - Catalysis of L-cysteine by IscS in the presence of IscU

Jupyter Notebook - 55.2 KB -

Used to model the given OMEX EnzymeML archive using the Python package lmfit.

Desulfuration_Cysteine_Pinto_input_interferENZY.txt

Feb 15, 2022 - Catalysis of L-cysteine by IscS in the presence of IscU

Plain Text - 370 B -

Text file that is used as input for InterferEnzy

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