Institute of Biochemistry

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1,031 to 1,040 of 1,292 Results

Analysis_Peptide_Unfolding.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 - 6.0 KB - MD5: 083105216742702a9cd08fca114b8106 Python script to analyse the unfolding behavior of a peptide in a sMD simulation.
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.
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_Peptide_Unfolding.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 - 6.0 KB -

Python script to analyse the unfolding behavior of a peptide in a sMD simulation.

Analysis_RMSD-C_N_Distance_Correlation.py

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.

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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