A Structure-Based Pipeline for Targeting the Long Non-Coding RNA MALAT1

Data for molecular dynamics (MD) simulations and molecular docking calculations on the triple-helix structure of the MALAT1 RNA. The input_output_MDsimulations.zip file contains input files to perform both plain (i.e. unbiased) and Hamiltonian replica-exchange (hREX) MD simulations, as well as the corresponding output trajectories. The malat1_analyses.tar.gz file contains all RNA and ligand structures for docking via AutoDock-GPU and rDock, as well as output data to perform analysis of results. The Notebook_malat1.ipynb Jupyter Notebook illustrates how to perform all the analyses; the notebook should be run under the malat1 conda environment, which can be installed using the environment.yml file. A tree.txt file is provided to help navigating the five main subfolders: - The folder pocketron_malat1/ contains all outputs produced by Pocketron, including the pocket–residue matrices, the communication-network files, and all intermediate data generated for the analysis- The folder data_trj/ stores MD trajectories and the corresponding reference PDB structures used for the analyses reported in the notebook. It contains both the unbiased and HREX simulations for RMSD/eRMSD calculations, PCA and centroid extraction- The folder data_docking/ contains all docking-related materials, organized into: i) input files, divided into AutoDock and rDock inputs, together with the original conformations extracted from the MD ensemble for both binding sites; ii) site-specific directories (site1/ and site2/), containing complete results for every ligand across all conformations, with separate subfolders for AutoDock-GPU and rDock outputs that include rescoring results obtained using multiple scoring functions, and PCA directories storing the data for the principal component analyses performed on the docking results for each site- The folder data_fingernat/ contains all FingeRNAt interaction-fingerprint results for both binding sites. For each site, three subfolders provide: i) the global FingeRNAt results for all poses, ii) clustering results, and iii) FingeRNAt results computed only for the selected clusters retained for PCA and regression analyses- The folder data_plots/ stores all variables and data structures saved in pickle binary format during the notebook-based analyses The notebook for the analyses can also be straightforwardly consulted at https://github.com/CompMedChemLab/project_malat1本数据集面向MALAT1 RNA三股螺旋结构的分子动力学（Molecular Dynamics, MD）模拟及分子对接计算相关研究。 input_output_MDsimulations.zip 压缩包包含可执行普通（即无偏）哈密顿副本交换（Hamiltonian Replica-Exchange, hREX）两种分子动力学模拟的输入文件，以及对应输出的轨迹文件。 malat1_analyses.tar.gz 压缩包涵盖用于AutoDock-GPU与rDock对接的全部RNA及配体结构，同时包含用于结果分析的输出数据。Notebook_malat1.ipynb 为Jupyter Notebook文件，演示了全部分析流程的执行方法；该脚本需在malat1的Conda环境中运行，可通过environment.yml文件完成环境部署。本次数据集附带tree.txt文件，用于辅助浏览以下5个主要子文件夹： - pocketron_malat1/ 文件夹存储Pocketron生成的全部输出结果，包括口袋-残基矩阵、通信网络文件，以及分析过程中产生的所有中间数据 - data_trj/ 文件夹存储本数据集分析中用到的分子动力学轨迹与对应参考PDB结构，包含用于均方根偏差（Root Mean Square Deviation, RMSD）/有效均方根偏差（effective RMSD, eRMSD）计算、主成分分析（Principal Component Analysis, PCA）以及质心提取的无偏与hREX模拟数据 - data_docking/ 文件夹包含全部对接相关材料，具体分为：① 输入文件：分为AutoDock与rDock两类输入，同时包含从两个结合位点的分子动力学集合中提取的原始构象；② 位点专属目录（site1/与site2/）：存储所有配体在全部构象下的完整对接结果，其中包含AutoDock-GPU与rDock输出结果的独立子文件夹（内含基于多种打分函数得到的重打分结果），以及用于存储各站点对接结果主成分分析数据的PCA子目录 - data_fingernat/ 文件夹存储两个结合位点的全部FingeRNAt相互作用指纹结果。针对每个位点，下设3个子文件夹分别提供：① 所有对接构象的全局FingeRNAt分析结果；② 聚类分析结果；③ 仅针对主成分分析与回归分析所保留的选定聚类所计算得到的FingeRNAt结果 - data_plots/ 文件夹存储基于Jupyter Notebook进行分析过程中，以Pickle二进制格式保存的全部变量与数据结构 本次分析所用的Jupyter Notebook脚本也可通过以下链接直接查阅：https://github.com/CompMedChemLab/project_malat1