MD Simulations

Featured Dataverses

In order to use this feature you must have at least one published or linked dataverse.

Publish Dataverse

Are you sure you want to publish your dataverse? Once you do so it must remain published.

Publish Dataverse

This dataverse cannot be published because the dataverse it is in has not been published.

Delete Dataverse

Are you sure you want to delete your dataverse? You cannot undelete this dataverse.

51 to 60 of 72 Results

Zinc.pdb Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation application/vnd.palm - 1.5 KB - MD5: d0faeef5a7789400011fa63d86b86947
ZNB.xml Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation XML - 1.6 KB - MD5: a8f183de30b9a05bd6a6515d639ea88c Parameters for the Zink-Dummy model.
Movie1_ssK36_hairpin_formation.mp4 Aug 15, 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 MPEG-4 Video - 7.9 MB - MD5: bc370cb514eda10a067eaff28bc80a26 Formation of hairpin conformation of ssK36 peptide. The movie shows an MD simulation of the ssK36 peptide in solution and its formation of a hairpin conformation.
Movie2_sMD_ssK36_successfull_binding.mp4 Aug 15, 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 MPEG-4 Video - 15.2 MB - MD5: bc3201d5df0f95885e3c4c14f73bc92a Representative sMD simulation without repulsive force. The movie shows the ssK36 peptide approaching SETD2 in a hairpin conformation and afterwards successfully establishing a TS-like structure.
Movie3_sMD_H3K36_unsuccessfull_binding.mp4 Aug 15, 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 MPEG-4 Video - 16.3 MB - MD5: 72b0b55bd9fdecbca087667e52ff69c7 Representative sMD with repulsive force. The movie shows the H3K36 peptide approaching SETD2 in an extended conformation. Afterwards, it fails to establish a transition-state like structure.
Movie4_sMD_ssK36_unfolding.mp4 Aug 15, 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 MPEG-4 Video - 20.0 MB - MD5: b86d4c5b5dd1809e83e12116fd8b8b66 Representative sMD without repulsive force showing peptide unfolding during the binding process. The ssK36 peptide enters the SETD2 binding cleft in a hairpin conformation and afterwards unfolds into an extended structure similarly as the structure observed in the crystal structure.
SETD2 MD Data.xlsx Aug 15, 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 MS Excel Spreadsheet - 572.3 KB - MD5: b0809a96189ad4f9d583abeffe0955f4 Data presented in the manuscript.
Analysis_Contact_Maps_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 - 2.0 KB - MD5: b0a2caadbfb0c6ae3e16e468810d8c2e Follow-up python script for "Analysis_Contact_Maps.py"
Analysis_Contact_Maps.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 - 8.1 KB - MD5: 7bf709c86e3e19e740e6f74ca723efa6 Python script to analyse the contacts of a trajectory (needs follow up script "Analysis_Contact_Maps_Analysis.py").
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.

Zinc.pdb

Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

application/vnd.palm - 1.5 KB -

ZNB.xml

Mar 14, 2023 - Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

XML - 1.6 KB -

Parameters for the Zink-Dummy model.

Movie1_ssK36_hairpin_formation.mp4

Aug 15, 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

MPEG-4 Video - 7.9 MB -

Formation of hairpin conformation of ssK36 peptide. The movie shows an MD simulation of the ssK36 peptide in solution and its formation of a hairpin conformation.

Movie2_sMD_ssK36_successfull_binding.mp4

MPEG-4 Video - 15.2 MB -

Representative sMD simulation without repulsive force. The movie shows the ssK36 peptide approaching SETD2 in a hairpin conformation and afterwards successfully establishing a TS-like structure.

Movie3_sMD_H3K36_unsuccessfull_binding.mp4

MPEG-4 Video - 16.3 MB -

Representative sMD with repulsive force. The movie shows the H3K36 peptide approaching SETD2 in an extended conformation. Afterwards, it fails to establish a transition-state like structure.

Movie4_sMD_ssK36_unfolding.mp4

MPEG-4 Video - 20.0 MB -

Representative sMD without repulsive force showing peptide unfolding during the binding process. The ssK36 peptide enters the SETD2 binding cleft in a hairpin conformation and afterwards unfolds into an extended structure similarly as the structure observed in the crystal structure.

SETD2 MD Data.xlsx

MS Excel Spreadsheet - 572.3 KB -

Data presented in the manuscript.

Analysis_Contact_Maps_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 - 2.0 KB -

Follow-up python script for "Analysis_Contact_Maps.py"

Analysis_Contact_Maps.py

Plain Text - 8.1 KB -

Python script to analyse the contacts of a trajectory (needs follow up script "Analysis_Contact_Maps_Analysis.py").

Analysis_Peptide_Unfolding.py

Plain Text - 6.0 KB -

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

Add Data

Share Dataverse

Link Dataverse

Reset Modifications