Institute of Biochemistry

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1 to 10 of 1,772 Results

Contact_maps_allosteric_substrate_peptide.py Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity Python Source Code - 34.9 KB - MD5: 97c014ab186bedf14d56837faddea3c5 Python script to analyse the contacts in a MD trajectory.
Contact_maps_analysis.py Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity Python Source Code - 6.0 KB - MD5: 8b61a964a898773f4d8af86a1ba501c6 Python script for the subsequent analysis of the contact maps analysin python script.
Contact_maps.py Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity Python Source Code - 34.9 KB - MD5: d1e956e38859db292bd5ffd7c53f7749 Python script to analyse the contacts in a MD trajectory.
Contact_maps_sidechains.py Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity Python Source Code - 35.2 KB - MD5: da2bd50f8e772a853956584924b1edf3 Python script to analyse the contacts in a MD trajectory.
gaff.xml Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity XML - 537.3 KB - MD5: cf54909804c6ee0eba7d03b93df3cef4 The employed force field.
get_knick_angle.py Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity Python Source Code - 4.1 KB - MD5: 6becca1cc33b82fc1bbf16b31f324261 Python code to analyse the bending of the SMYD1 CTD during 500 ns MD simulation.
Histograms.ipynb Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity Jupyter Notebook - 113.9 KB - MD5: f3abf36ffa1d94aca23185719eda2634 Jupyter Notebook to analyse the results of the SN2 analysis.
Movie 1 Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity Quicktime Video - 4.6 MB - MD5: f9ed24b6e99176b2b1442bc02d07c36d Exemplary MD simulation of SMYD1 with CTH in extended conformation with MYH2 (124-138) and addition of a second MYH2 (124-138) as allosteric peptide. 11 ns (204 ns-215 ns) movie of a sliced 500 ns MD trajectory showing SMYD1 complexed with two molecules of the MYH2 (124-138) peptide bound in the substrate and allosteric peptide sites. Initially, th...
Movie 2 Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity Quicktime Video - 82.7 MB - MD5: 32323298a3d331618e292dff90a0558c Exemplary MD simulation of SMYD1 with CTH in bent conformation with MYH2 (124-154). 20 ns (30 ns - 50 ns) movie snippet from a 100 ns MD simulation of SMYD1 complexed with the MYH2 (124-154) substrate. The C-terminal helix is in the bent conformation. The movie shows the stable docking of the C-terminal part of MYH2 (124-154) into the allosteric pe...
production_SMYD1_MYH2_CTD_bent_100ns_1.pdb Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity application/vnd.palm - 637.5 KB - MD5: 59885e53c7b4b012ee4a33d195ea8d9b

Contact_maps_allosteric_substrate_peptide.py

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

Python Source Code - 34.9 KB -

Python script to analyse the contacts in a MD trajectory.

Contact_maps_analysis.py

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

Python Source Code - 6.0 KB -

Python script for the subsequent analysis of the contact maps analysin python script.

Contact_maps.py

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

Python Source Code - 34.9 KB -

Python script to analyse the contacts in a MD trajectory.

Contact_maps_sidechains.py

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

Python Source Code - 35.2 KB -

Python script to analyse the contacts in a MD trajectory.

gaff.xml

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

XML - 537.3 KB -

The employed force field.

get_knick_angle.py

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

Python Source Code - 4.1 KB -

Python code to analyse the bending of the SMYD1 CTD during 500 ns MD simulation.

Histograms.ipynb

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

Jupyter Notebook - 113.9 KB -

Jupyter Notebook to analyse the results of the SN2 analysis.

Movie 1

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

Quicktime Video - 4.6 MB -

Exemplary MD simulation of SMYD1 with CTH in extended conformation with MYH2 (124-138) and addition of a second MYH2 (124-138) as allosteric peptide. 11 ns (204 ns-215 ns) movie of a sliced 500 ns MD trajectory showing SMYD1 complexed with two molecules of the MYH2 (124-138) peptide bound in the substrate and allosteric peptide sites. Initially, th...

Movie 2

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

Quicktime Video - 82.7 MB -

Exemplary MD simulation of SMYD1 with CTH in bent conformation with MYH2 (124-154). 20 ns (30 ns - 50 ns) movie snippet from a 100 ns MD simulation of SMYD1 complexed with the MYH2 (124-154) substrate. The C-terminal helix is in the bent conformation. The movie shows the stable docking of the C-terminal part of MYH2 (124-154) into the allosteric pe...

production_SMYD1_MYH2_CTD_bent_100ns_1.pdb

Oct 1, 2026 - Additional Data related to Dorscht and Schnee et al.: Bending into action: C-terminal helix bending and recognition of an extended substrate sequence controls SMYD1 activity

application/vnd.palm - 637.5 KB -

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