PySteMoDA Datasets

The source code for the software package PySteMoDA is already available at : https://zenodo.org/records/18258018 This dataset includes the output files of NAMD simulations of mmCdh23EC19-20 and ICAM1 . Cadherin-23 (CDH23) subdomain including extracellular cadherin (EC) repeats EC19-20 with three bound calcium ions (extracted from PDB: 5TFK and hereafter referred to as CDH23 EC19-20). Simulations of the CDH23 EC19-20 system ( = 244,076 atoms) were performed using NAMD 2.12 with the CHARMM36 force field and the TIP3P water model. Van der Waals forces were computed using a 12 Å cutoff with a switching function starting at 10 Å. Electrostatic forces were computed using the particle mesh Ewald algorithm with a grid spacing of 1 Å. Dynamics in time was advanced using a 2 fs timestep. The system was first minimized for 1,000 steps, then subjected to 50,000 steps of constrained backbone dynamics (k ~ 700 pN/nm). A Langevin thermostat and hybrid Nosé-Hoover piston method were used to maintain a temperature of 300 K and pressure of 1 atmosphere (NpT ensemble). In the first 1 ns a Langevin damping coefficient of 1 ps-1 was used for the thermostat while in the following 10 ns a Langevin damping coefficient of 0.1 ps-1 was used. A piston period of 200 fs and a damping timescale of 100 fs were used for pressure control. For SMD simulations, virtual springs were attached to the N- and C-terminal Cα atoms with spring constants of k ~ 700 pN/nm. The free ends of the virtual springs were moved at stretching speeds of 5 nm/ns in opposite directions. SMD data output and coordinates were written to disk every 40 fs and every 1 ps, respectively. The second set of simulations used to validate and showcase PySteMoDA involved the intercellular adhesion molecule 1 (ICAM-1, = 67,215) which was simulated with NAMD 2.9 using the CHARMM36 force field and the TIP3P water model. Dynamics in time were advanced using a 2 fs timestep. The results are reported in the supplementary material. We modelled ICAM-1 based on the cryo-EM structure of D1-D5 (PDB ID: 1Z7Z) and crystal structure of D3-D5 (PDB ID: 2OZ4) . Disulfide bonds were specified using the corresponding patch to create the protein structure file (PSF) for simulation. ICAM-1 was stretched at 1 nm/ns along a direction defined by the vector that connected the fixed and SMD atoms after equilibration. The N-terminal Cɑ atom was fixed during the simulation. The spring constant corresponds to 104 pN/nm. The simulation was carried out over a total of 70 ns with outputs written every 10 ps for both DCD (trajectory coordinates) and SMD frequencies. In the case of the ICAM-1, the simulation was conducted in the NVE ensemble, where the number of particles, volume, and total energy were conserved throughout the run. Extended data is available along with the underlaying data within the file below : EXTENDED_DATA_Supp_material_PySteMoDA_v2.docx