Department of Molecular Biochemistry

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1 to 10 of 852 Results

MD Simulations with PRDM9 May 22, 2025 - MD Simulations Jeltsch, Albert; Schnee, Philipp, 2025, "MD Simulations with PRDM9", https://doi.org/10.18419/DARUS-4567, DaRUS, V2 This data collection contains additional data related to Graf et al.: "Investigation and design of the dual specificity of the PRDM9 protein lysine methyltransferase". This includes: Modelled structures of PRDM9 bound to different peptides Source data of the results of the MD analysis MD simulations codes and analysis scripts
PRDM9_production_updated.py May 22, 2025 - MD Simulations with PRDM9 Python Source Code - 14.6 KB - MD5: 4e96dbf12d690fccfb42a03bb46b50ea Python script for the production of MD simulations of PRDM9 complexed with a peptide
PRDM9_AdoMet.pdb Apr 28, 2025 - MD Simulations with PRDM9 application/vnd.palm - 2.8 KB - MD5: 06725e1c633711c73ee4debdbd5d1498 PDB file of AdoMet cofactor
PRDM9_Analysis-SN2-Transition_States.py Apr 28, 2025 - MD Simulations with PRDM9 Python Source Code - 3.1 KB - MD5: 5372ebbaced32905de678aa61df0589f Python script to analyse the SN2 transition state-like conformations in a MD trajectory.
PRDM9_contact_maps_analysis.py Apr 28, 2025 - MD Simulations with PRDM9 Python Source Code - 4.5 KB - MD5: dc866effb0715ec46b6399e49ed330e7 Python script for the subsequent analysis of the contact maps analysin python script
PRDM9_contacts_single.py Apr 28, 2025 - MD Simulations with PRDM9 Python Source Code - 8.3 KB - MD5: c2f250b0579f0ce221c2fb029085539f Python script to analyse the contacts in a MD trajectory
PRDM9_H3K36_starting_structure.pdb Apr 28, 2025 - MD Simulations with PRDM9 application/vnd.palm - 220.6 KB - MD5: 62734a1811fb6c56b0a60c8138d055a3 PDB file for PRDM9 complexed with the 15 amino acid long H3K4 peptide
PRDM9_H3K4_starting_structure.pdb Apr 28, 2025 - MD Simulations with PRDM9 application/vnd.palm - 220.3 KB - MD5: b542e94a21a3473c19d3f978f95402e7 PDB file for PRDM9 complexed with the 15 amino acid long H3K4 peptide
PRDM9_ZNB.pdb Apr 28, 2025 - MD Simulations with PRDM9 application/vnd.palm - 509 B - MD5: d380a5863e9f01b055de5d4695ef235a PDB file of Zink ion for structural stability
README.pdf Apr 28, 2025 - MD Simulations with PRDM9 Adobe PDF - 288.7 KB - MD5: 1590d95381b47eeef3ffddf9345b8783 README file to guide you through this repository and explain all contents.

MD Simulations with PRDM9

May 22, 2025 - MD Simulations

Jeltsch, Albert; Schnee, Philipp, 2025, "MD Simulations with PRDM9", https://doi.org/10.18419/DARUS-4567, DaRUS, V2

This data collection contains additional data related to Graf et al.: "Investigation and design of the dual specificity of the PRDM9 protein lysine methyltransferase". This includes: Modelled structures of PRDM9 bound to different peptides Source data of the results of the MD analysis MD simulations codes and analysis scripts

PRDM9_production_updated.py

May 22, 2025 - MD Simulations with PRDM9

Python Source Code - 14.6 KB -

Python script for the production of MD simulations of PRDM9 complexed with a peptide

PRDM9_AdoMet.pdb