dynamicPDB

Dynamic PDB 是一个大规模的蛋白质动态行为数据集，旨在通过整合动态数据和额外的物理属性，增强现有的权威静态3D蛋白质结构数据库，如蛋白质数据银行（PDB）。该数据集包含约12,600个经过筛选的蛋白质，每个蛋白质都接受了全原子分子动力学（MD）模拟，以捕捉其构象变化。与先前的蛋白质MD数据集相比，Dynamic PDB 提供了三个关键进步：更长的模拟持续时间（每种蛋白质长达1微秒）、更精细的时间间隔（1皮秒）以及更丰富的物理属性（包括原子速度、力、势能/动能和模拟环境温度等）。

Dynamic PDB is a large-scale dataset of protein dynamic behaviors, which aims to enhance existing authoritative static 3D protein structure databases such as the Protein Data Bank (PDB) by integrating dynamic data and additional physical properties. This dataset contains approximately 12,600 screened proteins, each of which has undergone all-atom molecular dynamics (MD) simulations to capture its conformational changes. Compared with previous protein MD datasets, Dynamic PDB offers three key advancements: longer simulation duration (up to 1 microsecond per protein), finer time intervals (1 picosecond), and richer physical properties including atomic velocity, force, potential/kinetic energy, and simulation environment temperature, among others.