Dataset for "In silico Positional Analogue Scanning with Amber GPU-TI"

This repository contains the full data set and analysis scripts to reproduce all results for the manuscript "<strong>In silico Positional Analogue Scanning with Amber GPU-TI</strong>, <em>J. Chem. Inf. Model.</em> 2022, 62, 18, 4448–4459". https://doi.org/10.1021/acs.jcim.2c00860 <br> The repository contains the following data: <strong>20_PDB_66_MOL2_input_coordinates_for_PAS.tar.gz (7.7MB)</strong> input structures of proteins (pdb format), ligands (mol2 format), experimental data and GPU-TI maps for all the 20 scans including Br-Scan, Cl-Scan, F-Scan, HO-Scan, MeO-Scan, Me-Scan, N-Scan. <strong>AMBER18.GPUTI.scripts.tar.gz (597.2 M)</strong> Scripts and example of CDK8 TI output for GPU TI ddG calculation and cycle closure correlation. <strong>Supporting_Information_Tables_dG_ddG_small_big_change.xlsx (60kB)</strong> AMBER18_input_fort files, parameter and topology files, first 500 ps equilibrated restart files, amber TI input files for each TI pair calculations (total 12.9 GB) <strong>AMBER-GPUTI_PAS_input.01.N-Scan.CDK8.tar.gz (736.2MB)</strong> <strong>AMBER-GPUTI_PAS_input.02.N-Scan.Tankyrase.tar.gz (266.1 MB)</strong> <strong>AMBER-GPUTI_PAS_input.03.N-Scan.HCV_NS5B_gt1b.tar.gz (722.6 MB)</strong> <strong>AMBER-GPUTI_PAS_input.04.F-Scan.ox1r_antagonist.tar.gz (549.4 MB)</strong> <strong>AMBER-GPUTI_PAS_input.05.F-Scan.ox2r_antagonist.tar.gz (768.4 MB)</strong> <strong>AMBER-GPUTI_PAS_input.06.F-Scan.KAT6A.tar.gz (407.9 MB)</strong> <strong>AMBER-GPUTI_PAS_input.07.F-Scan.PDE1B.tar.gz (470.7 MB)</strong> <strong>AMBER-GPUTI_PAS_input.08.F-Scan.Akt1_kinase.tar.gz (390.6 MB)</strong> <strong>AMBER-GPUTI_PAS_input.09.Cl-Scan.PPAR_Gama.tar.gz (412.9 MB)</strong> <strong>AMBER-GPUTI_PAS_input.10.Cl-Scan.erk12.tar.gz (352.4 MB)</strong> <strong>AMBER-GPUTI_PAS_input.11.Cl-Scan.KAT6A.tar.gz (408.2 MB)</strong> <strong>AMBER-GPUTI_PAS_input.12.Br-Scan.PRMT4.tar.gz (522.1 MB)</strong> <strong>AMBER-GPUTI_PAS_input.13.Me-Scan.BD1_scaffold_thiophene.tar.gz (187.6 MB)</strong> <strong>AMBER-GPUTI_PAS_input.14.Me-Scan.BD1_scaffold_furan.tar.gz (187.3 MB)</strong> <strong>AMBER-GPUTI_PAS_input.15.Me-Scan.HIV-1.tar.gz (740.2 MB)</strong> <strong>AMBER-GPUTI_PAS_input.16.Me-Scan.PPAR_Gama.tar.gz (412.8 MB)</strong> <strong>AMBER-GPUTI_PAS_input.17.Me-Scan.avb6.tar.gz (2.2 GB)</strong> <strong>AMBER-GPUTI_PAS_input.18.MeO-Scan.KAT6A.tar.gz (409.3 MB)</strong> <strong>AMBER-GPUTI_PAS_input.19.MeO-Scan.ox2r_agonist.tar.gz (1.1 GB)</strong> <strong>AMBER-GPUTI_PAS_input.20.HO-Scan.ox2r_agonist.tar.gz (1.1 GB)</strong><br> <strong>Data Structures inside each files:</strong> <strong>directory_tree.20_PDB_66_MOL2_input_coordinates_for_PAS.txt (5 kB)</strong> <strong>directory_tree.AMBER18.GPUTI.scripts.txt (91 kB)</strong> <strong>directory_tree.AMBER18_input_for_PAS_GPUTI_simulations.txt (1.5 MB)</strong>本仓库收录完整数据集与分析脚本，可复现论文**《基于Amber GPU-TI的计算机模拟位置类似物扫描》（In silico Positional Analogue Scanning with Amber GPU-TI）**，该论文发表于《Journal of Chemical Information and Modeling》（缩写*J. Chem. Inf. Model.*）2022年第62卷第18期，页码4448–4459，DOI：10.1021/acs.jcim.2c00860。 本仓库包含如下数据： 1. **20_PDB_66_MOL2_input_coordinates_for_PAS.tar.gz（7.7 MB）**：包含20组位置类似物扫描（Positional Analogue Scanning，PAS）所需的输入数据，涵盖溴代扫描、氯代扫描、氟代扫描、羟基扫描、甲氧基扫描、甲基扫描、氮取代扫描，内含蛋白质输入结构（PDB格式）、配体输入结构（MOL2格式）、实验数据以及GPU-TI图谱。 2. **AMBER18.GPUTI.scripts.tar.gz（597.2 MB）**：包含用于GPU-TI自由能变化差（ddG）计算以及循环闭合相关性分析的脚本，以及CDK8的TI输出示例文件。 3. **Supporting_Information_Tables_dG_ddG_small_big_change.xlsx（60 KB）**：包含AMBER18输入文件（fort格式）、参数与拓扑文件、前500皮秒（ps）平衡后的重启文件，以及每一组TI对计算所用的Amber TI输入文件，总大小12.9 GB。 4. **AMBER-GPUTI_PAS_input.01.N-Scan.CDK8.tar.gz（736.2 MB）** 5. **AMBER-GPUTI_PAS_input.02.N-Scan.Tankyrase.tar.gz（266.1 MB）** 6. **AMBER-GPUTI_PAS_input.03.N-Scan.HCV_NS5B_gt1b.tar.gz（722.6 MB）** 7. **AMBER-GPUTI_PAS_input.04.F-Scan.ox1r_antagonist.tar.gz（549.4 MB）** 8. **AMBER-GPUTI_PAS_input.05.F-Scan.ox2r_agonist.tar.gz（768.4 MB）** 9. **AMBER-GPUTI_PAS_input.06.F-Scan.KAT6A.tar.gz（407.9 MB）** 10. **AMBER-GPUTI_PAS_input.07.F-Scan.PDE1B.tar.gz（470.7 MB）** 11. **AMBER-GPUTI_PAS_input.08.F-Scan.Akt1_kinase.tar.gz（390.6 MB）** 12. **AMBER-GPUTI_PAS_input.09.Cl-Scan.PPAR_Gama.tar.gz（412.9 MB）** 13. **AMBER-GPUTI_PAS_input.10.Cl-Scan.erk12.tar.gz（352.4 MB）** 14. **AMBER-GPUTI_PAS_input.11.Cl-Scan.KAT6A.tar.gz（408.2 MB）** 15. **AMBER-GPUTI_PAS_input.12.Br-Scan.PRMT4.tar.gz（522.1 MB）** 16. **AMBER-GPUTI_PAS_input.13.Me-Scan.BD1_scaffold_thiophene.tar.gz（187.6 MB）** 17. **AMBER-GPUTI_PAS_input.14.Me-Scan.BD1_scaffold_furan.tar.gz（187.3 MB）** 18. **AMBER-GPUTI_PAS_input.15.Me-Scan.HIV-1.tar.gz（740.2 MB）** 19. **AMBER-GPUTI_PAS_input.16.Me-Scan.PPAR_Gama.tar.gz（412.8 MB）** 20. **AMBER-GPUTI_PAS_input.17.Me-Scan.avb6.tar.gz（2.2 GB）** 21. **AMBER-GPUTI_PAS_input.18.MeO-Scan.KAT6A.tar.gz（409.3 MB）** 22. **AMBER-GPUTI_PAS_input.19.MeO-Scan.ox2r_agonist.tar.gz（1.1 GB）** 23. **AMBER-GPUTI_PAS_input.20.HO-Scan.ox2r_agonist.tar.gz（1.1 GB）** **各文件内的数据结构如下**： - **directory_tree.20_PDB_66_MOL2_input_coordinates_for_PAS.txt（5 KB）** - **directory_tree.AMBER18.GPUTI.scripts.txt（91 KB）** - **directory_tree.AMBER18_input_for_PAS_GPUTI_simulations.txt（1.5 MB）**