MD Simulations

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11 to 20 of 77 Results

SAM.xml Apr 28, 2025 - MD Simulations with PRDM9 XML - 20.9 KB - MD5: 8504b192cebc39de3edb5595d94cd0e4 Parameter file for cofactor SAM
ZNB.xml Apr 28, 2025 - MD Simulations with PRDM9 XML - 1.6 KB - MD5: a8f183de30b9a05bd6a6515d639ea88c Parameter file for zinc ions
Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate Mar 28, 2024 Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen; Weirich, Sara, 2024, "Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate", https://doi.org/10.18419/DARUS-3815, DaRUS, V1 This data collection contains additional data related to Weirich et al.: "Discovery of new NSD2 non-histone substrates and design of a super-substrate". This includes Modelled structures of NSD2 bound to different peptides Source data of the results of the MD analysis MD simulations codes and analysis scripts
Analysis-SN2-Transition_States.py Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate Python Source Code - 3.3 KB - MD5: 7e56f5ea455fdaf01d765c2eedd0fd35 Python script to analyse the SN2 transition states in a MD trajectory.
contact_map_explorer.py Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate Python Source Code - 9.6 KB - MD5: fd944dbf9f26ebc03682972be3b472b6 Python script to analyse the contacts in a MD trajectory
MD SourceData_P30G_P43S.xlsx Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate MS Excel Spreadsheet - 105.8 KB - MD5: 9cbfc909c7a116f2f774327b9b857798 Source Data for the conducted MD simulation experiments with the P30G/P43S mutant
MD SourceData.xlsx Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate MS Excel Spreadsheet - 195.0 KB - MD5: 4012b61efae90eac1b3485438cf56853 Source Data for the conducted MD simulation experiments
Movie_NSD2_ssK36.mp4 Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate MPEG-4 Video - 12.9 MB - MD5: dda465d0d937f1d25e48f0bfb27ce073 This is a movie of a MD simulation run section of NSD2 complexed with the ssK36 peptide and AdoMet.
NSD2_H3K36_end_structure.pdb Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate application/vnd.palm - 158.1 KB - MD5: d946cb57a0cce7d30d71f96bd969fdd9 PDB file of exemplary conformation of NSD2 complexed with the 15 amino acid long H3K36 peptide after 100 ns MD simulation.
NSD2_H3K36_P30G_P43S.pdb Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate application/vnd.palm - 153.2 KB - MD5: e553c259718b03d4595102d753b240f0 PDB file of NSD2 complexed with H3K36 P30G/P43S mutant peptide

SAM.xml

Apr 28, 2025 - MD Simulations with PRDM9

XML - 20.9 KB -

Parameter file for cofactor SAM

ZNB.xml

Apr 28, 2025 - MD Simulations with PRDM9

XML - 1.6 KB -

Parameter file for zinc ions

Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate

Mar 28, 2024

Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen; Weirich, Sara, 2024, "Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate", https://doi.org/10.18419/DARUS-3815, DaRUS, V1

This data collection contains additional data related to Weirich et al.: "Discovery of new NSD2 non-histone substrates and design of a super-substrate". This includes Modelled structures of NSD2 bound to different peptides Source data of the results of the MD analysis MD simulations codes and analysis scripts

Analysis-SN2-Transition_States.py

Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate

Python Source Code - 3.3 KB -

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

contact_map_explorer.py

Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate

Python Source Code - 9.6 KB -

Python script to analyse the contacts in a MD trajectory

MD SourceData_P30G_P43S.xlsx

Mar 28, 2024 - Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate

MS Excel Spreadsheet - 105.8 KB -

Source Data for the conducted MD simulation experiments with the P30G/P43S mutant