MD Simulations with PRDM9

Version 2.0

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

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Description	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
Subject	Chemistry; Computer and Information Science; Medicine, Health and Life Sciences
Keyword	Protein Methyltransferases, Enzyme Specificity
Related Publication	Is Supplement To: Graf et al.: "Investigation and design of the dual specificity of the PRDM9 protein lysine methyltransferase". Communications Biology, 2025.doi: 10.1038/s42003-025-08207-4
Notes	More information can be found in the README.pdf.
Data Generation	Simulation; Analysis; Experiment
License/Data Use Agreement	Custom Dataset Terms

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	1 to 10 of 11 Files	Download
	README.pdf Adobe PDF - 288.7 KB Published Apr 28, 2025 2 Downloads MD5: 1590d95381b47eeef3ffddf9345b8783 README file to guide you through this repository and explain all contents.	Preview "README.pdf" Access File File Access Public Download Options Adobe PDF Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PRDM9_Analysis-SN2-Transition_States.py Python_scripts/Python Source Code - 3.1 KB Published Apr 28, 2025 0 Downloads MD5: 5372ebbaced32905de678aa61df0589f Python script to analyse the SN2 transition state-like conformations in a MD trajectory.	Access File File Access Public Download Options Python Source Code Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PRDM9_contacts_single.py Python_scripts/Python Source Code - 8.3 KB Published Apr 28, 2025 0 Downloads MD5: c2f250b0579f0ce221c2fb029085539f Python script to analyse the contacts in a MD trajectory	Access File File Access Public Download Options Python Source Code Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PRDM9_contact_maps_analysis.py Python_scripts/Python Source Code - 4.5 KB Published Apr 28, 2025 0 Downloads MD5: dc866effb0715ec46b6399e49ed330e7 Python script for the subsequent analysis of the contact maps analysin python script	Access File File Access Public Download Options Python Source Code Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PRDM9_production_updated.py Python_scripts/Python Source Code - 14.6 KB Published May 22, 2025 0 Downloads MD5: 4e96dbf12d690fccfb42a03bb46b50ea Python script for the production of MD simulations of PRDM9 complexed with a peptide	Access File File Access Public Download Options Python Source Code Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PRDM9_AdoMet.pdb Simulation_starting_files/application/vnd.palm - 2.8 KB Published Apr 28, 2025 0 Downloads MD5: 06725e1c633711c73ee4debdbd5d1498 PDB file of AdoMet cofactor	Access File File Access Public Download Options application/vnd.palm Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PRDM9_H3K36_starting_structure.pdb Simulation_starting_files/application/vnd.palm - 220.6 KB Published Apr 28, 2025 0 Downloads MD5: 62734a1811fb6c56b0a60c8138d055a3 PDB file for PRDM9 complexed with the 15 amino acid long H3K4 peptide	Access File File Access Public Download Options application/vnd.palm Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PRDM9_H3K4_starting_structure.pdb Simulation_starting_files/application/vnd.palm - 220.3 KB Published Apr 28, 2025 0 Downloads MD5: b542e94a21a3473c19d3f978f95402e7 PDB file for PRDM9 complexed with the 15 amino acid long H3K4 peptide	Access File File Access Public Download Options application/vnd.palm Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	PRDM9_ZNB.pdb Simulation_starting_files/application/vnd.palm - 509 B Published Apr 28, 2025 0 Downloads MD5: d380a5863e9f01b055de5d4695ef235a PDB file of Zink ion for structural stability	Access File File Access Public Download Options application/vnd.palm Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	SAM.xml Simulation_starting_files/XML - 20.9 KB Published Apr 28, 2025 0 Downloads MD5: 8504b192cebc39de3edb5595d94cd0e4 Parameter file for cofactor SAM	Access File File Access Public Download Options XML Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX

Citation Metadata

Persistent Identifier	doi:10.18419/DARUS-4567
Publication Date	2025-04-28
Title	MD Simulations with PRDM9
Author	https://ror.org/04vnq7t770000-0001-6113-9290 https://ror.org/04vnq7t770000-0002-3731-9352
Point of Contact	Use email button above to contact. Jeltsch, Albert (University of Stuttgart)
Description	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
Subject	Chemistry; Computer and Information Science; Medicine, Health and Life Sciences
Keyword	Protein Methyltransferases http://www.wikidata.org/entity/Q58557455 (Wikidata) Enzyme Specificity http://www.wikidata.org/entity/Q1321568 (Wikidata)
Topic Classification	Biochemistry (LCSH) http://id.loc.gov/authorities/subjects/sh85014171 Molecular Dynamics Simulation (Wikidata) http://www.wikidata.org/entity/Q901663 Biochemistry (DFGFO) https://w3id.org/dfgfo/2024/211-01
Related Publication	Is Supplement To: Graf et al.: "Investigation and design of the dual specificity of the PRDM9 protein lysine methyltransferase". Communications Biology, 2025. doi 10.1038/s42003-025-08207-4 https://doi.org/10.1038/s42003-025-08207-4
Notes	More information can be found in the README.pdf.
Funding Information	DFG: EXC 2075 - 390740016
Depositor	Jeltsch, Albert
Deposit Date	2024-11-07
Data Type	Molecular models of protein structures; Primary data tables; MD simulations Python scripts; MD simulations analysis Python scripts

Process Metadata

Software

MD Traj Version: 1.9.4 (https://www.mdtraj.org/) LGPL v2.1+ (McGibbon, R. T., Beauchamp, K. A., Harrigan, M. P., Klein, C., Swails, J. M., Hernández, C. X., Schwantes, C. R., Wang, L.-P., Lane, T. J. & Pande, V. S. (2015). MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical Journal, 109, 1528-1532. doi: 10.1016/j.bpj.2015.08.015)
contact-map-explorer Version: 0.7.1 (https://contact-map.readthedocs.io/en/latest/index.html) LGPL-2.1 License
PyMol Version: 2.4.1 (https://pymol.org/2) LLC (The PyMOL Molecular Graphics System, Version 2.4.1 Schrödinger, LLC)
OpenMM Version: 7.5.1 (https://openmm.org/) MIT license (Eastman, P., Pande, V. S. (2010). OpenMM: A Hardware-Independent Framework for Molecular Simulations. Computing in Science & Engineering, 12 (4). PMCID: PMC4486654, doi: 10.1109/MCSE.2010.27)
Amber Tools Version: 18.0 (https://ambermd.org/AmberTools.php) GNU General Public License (GPL) (D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, N. Forouzesh, M. Ghazimirsaeed, G. Giambaşu, T. Giese, M.K. Gilson, H. Gohlke, A.W. Goetz, J. Harris, Z. Huang, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, A. Kovalenko, T. Kurtzman, T.S. Lee, P. Li, Z. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O'Hearn, A. Onufriev, F. Pan, S. Pantano, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, J. Wang, X. Wu, Y. Wu, Y. Xiong, Y. Xue, D.M. York, C. Zhao, Q. Zhu, and P.A. Kollman (2024), Amber 2024 Reference Manual, University of California, San Francisco. https://ambermd.org/doc12/Amber24.pdf)
PyMod Version: 3 (https://github.com/pymodproject/pymod) LGPL (Giacomo Janson, Alessandro Paiardini, PyMod 3: a complete suite for structural bioinformatics in PyMOL, Bioinformatics, Volume 37, Issue 10, 15 May 2021, Pages 1471-1472, doi: 10.1093/bioinformatics/btaa849)

Engineering Metadata

Data Generation	Simulation; Analysis; Experiment
Force Field	general AMBER force field (GAFF) https://ambermd.org/antechamber/gaff.html

Software Metadata (CodeMeta v2.0)

Software Version	Python 3.7
Development Status	Active
Runtime Platform	Python 3.7
Operating Systems	Ubuntu, Microsoft
Build Instructions	https://docs.conda.io/en/latest/miniconda.html
Software Requirements	numpy 1.21.5 https://numpy.org/ pandas 1.0.5 https://docs.python.org/3/library/itertools.html
Processor Requirements	GPUs, preferably NVIDIA
Storage Requirements	16 GB RAM, 200 GB SSD

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The research software (*.py) in this dataset is licensed under the MIT License.

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Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom terms specific to this dataset Custom Dataset Terms — the following Custom Dataset Terms have been defined for this dataset.

Terms of Use The research data in this dataset is licensed under the CC BY 4.0.
The research software (*.py) in this dataset is licensed under the MIT License.

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