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.docxPySteMoDA软件包的源代码已公开于链接：https://zenodo.org/records/18258018。 本数据集包含mmCdh23EC19-20与ICAM1的NAMD模拟输出文件。 钙粘蛋白-23（CDH23）亚结构域包含结合了三个钙离子的细胞外钙粘蛋白（EC）重复序列EC19-20，该结构提取自蛋白质数据库（Protein Data Bank，PDB）条目5TFK，下文简称CDH23 EC19-20。CDH23 EC19-20体系的原子数为244076，其模拟采用NAMD 2.12软件、CHARMM36力场与TIP3P水模型完成。范德华相互作用采用12 Å的截断半径，并以10 Å为起点施加切换函数进行计算；静电相互作用采用粒子网格埃瓦尔德算法，网格间距设置为1 Å。时间积分采用2 fs的时间步长。体系首先进行1000步能量最小化，随后执行50000步约束主链动力学模拟（力常数约为700 pN/nm）。采用朗之万恒温器与混合Nosé-Hoover活塞压控法维持体系温度300 K、压强1标准大气压，模拟处于NpT系综。模拟前1 ns的恒温器朗之万阻尼系数设为1 ps⁻¹，后续10 ns则调整为0.1 ps⁻¹。压强控制采用200 fs的活塞周期与100 fs的阻尼时间尺度。牵引分子动力学（Steered Molecular Dynamics, SMD）模拟中，虚拟弹簧连接至体系的N端与C端Cα原子，弹簧力常数约为700 pN/nm。虚拟弹簧的自由端以5 nm/ns的速率沿相反方向进行拉伸。SMD数据与坐标分别以每40 fs、每1 ps的间隔写入磁盘存储。 第二组用于验证并展示PySteMoDA性能的模拟体系为细胞间黏附分子1（ICAM-1，原子数67215），其模拟采用NAMD 2.9软件、CHARMM36力场与TIP3P水模型完成。时间积分采用2 fs的时间步长，相关模拟结果已发表于补充材料中。我们基于D1-D5结构的冷冻电镜结构（PDB ID: 1Z7Z）与D3-D5的晶体结构（PDB ID: 2OZ4）构建了ICAM-1的初始模型。通过对应的补丁命令指定二硫键，以生成模拟所需的蛋白质结构文件（Protein Structure File, PSF）。平衡完成后，沿固定原子与SMD原子的连线方向，以1 nm/ns的速率对ICAM-1进行拉伸。模拟过程中固定ICAM-1的N端Cα原子，所用弹簧的力常数为104 pN/nm。总模拟时长为70 ns，DCD（轨迹坐标）与SMD数据均以每10 ps的间隔写入输出文件。对于ICAM-1体系，模拟采用NVE系综进行，即整个模拟过程中粒子数、体积与总能量均保持守恒。 扩展数据与基础数据可随附文件获取：EXTENDED_DATA_Supp_material_PySteMoDA_v2.docx