Institute of Biochemistry

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1,541 to 1,550 of 1,834 Results

Analysis_RMSD-C_N_Distance_Correlation.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 - 7.1 KB - MD5: be9e0a85075a865bc8c8b9fab8f9f8bb Python script to analyse the correlation of RMSD and C-to-N-terminal distance of a trajectory. Intentionally used for sMD. (optional script)
Analysis_SN2-Transistion_States.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 - 3.6 KB - MD5: 56825bb781e96d9e4ac27d37222b7931 Python script to analyse the SN2 transition states in a trajectory.
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.

Analysis_RMSD-C_N_Distance_Correlation.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 - 7.1 KB -

Python script to analyse the correlation of RMSD and C-to-N-terminal distance of a trajectory. Intentionally used for sMD. (optional script)

Analysis_SN2-Transistion_States.py

Plain Text - 3.6 KB -

Python script to analyse the SN2 transition states in a trajectory.

Enspara_Clustering_Analysis.py

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.

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