DynaPIN Application Examples
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DynaPIN Test Cases This repository contains the Molecular Dynamics (MD) trajectories and validation data for the DynaPIN. It includes inputs and analysis outputs for an extended validation dataset of 12 protein complexes derived from Docking Benchmark v5.5, evenly spanning rigid, medium, and difficult targets. Directory Overview: Trajectory_Inputs/: Raw trajectory (.dcd) and topology (.pdb) files of test cases required to run the tool. DynaPIN_Outputs/: Pre-computed results organized into visualization figures, numerical tables (CSV data for metrics and properties), and processed structure files for each test case. Usage: Please refer to the DynaPIN GitHub Page for installation instructions. An example reproduction command is given below: dynapin --output_dir=6CWG_dynapin --trajectory_file=6CWG/production1.dcd --commands=all_analysis,all_plots --topology_file=6CWG/6CWG_input.pdb --stride=5 --foldx_path=your_foldx_path/
DynaPIN测试用例 本仓库包含面向DynaPIN的分子动力学（Molecular Dynamics）轨迹与验证数据，涵盖源自对接基准集v5.5（Docking Benchmark v5.5）的扩展验证数据集的输入文件与分析输出结果。该扩展验证集包含12个蛋白质复合物，均匀覆盖刚性、中等难度与高难度三类靶标。 目录概览： Trajectory_Inputs/：存放运行该工具所需的测试用例原始轨迹文件（.dcd格式）与拓扑结构文件（.pdb格式）。 DynaPIN_Outputs/：存放各测试用例的预计算结果，涵盖可视化图表、指标与属性的数值表格（CSV格式数据）以及经处理的结构文件。 使用方法： 请参阅DynaPIN官方GitHub页面获取安装指南。下文提供一条示例复现命令： dynapin --output_dir=6CWG_dynapin --trajectory_file=6CWG/production1.dcd --commands=all_analysis,all_plots --topology_file=6CWG/6CWG_input.pdb --stride=5 --foldx_path=your_foldx_path/
