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

<p>This repository contains the full data set and analysis scripts to reproduce all results for the manuscript &quot;<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.2c00860"><strong>In silico Positional Analogue Scanning with Amber GPU-TI</strong>,&nbsp;<em>J. Chem. Inf. Model.</em>&nbsp;2022, 62, 18, 4448&ndash;4459</a>&quot;.</p> <p><a href="https://doi.org/10.1021/acs.jcim.2c00860">https://doi.org/10.1021/acs.jcim.2c00860</a></p> <p><br> The repository contains the following data:</p> <ul> <li><strong>20_PDB_66_MOL2_input_coordinates_for_PAS.tar.gz&nbsp;(7.7MB)</strong> <ul> <li>input structures of proteins (pdb format),&nbsp;ligands (mol2 format), experimental data and&nbsp;GPU-TI maps&nbsp;for all the 20 scans including&nbsp;Br-Scan, Cl-Scan, F-Scan, HO-Scan, MeO-Scan, Me-Scan, N-Scan.</li> </ul> </li> <li><strong>AMBER18.GPUTI.scripts.tar.gz&nbsp;(597.2 M)</strong> <ul> <li>Scripts and example of CDK8 TI output for GPU TI ddG calculation&nbsp;and cycle closure correlation.</li> </ul> </li> <li><strong>Supporting_Information_Tables_dG_ddG_small_big_change.xlsx (60kB)</strong></li> <li>AMBER18_input_fort files, parameter and topology files, first 500 ps equilibrated restart files, amber TI input files for each TI pair calculations&nbsp;(total 12.9 GB) <ul> <li><strong>AMBER-GPUTI_PAS_input.01.N-Scan.CDK8.tar.gz&nbsp;(736.2MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.02.N-Scan.Tankyrase.tar.gz&nbsp;(266.1 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.03.N-Scan.HCV_NS5B_gt1b.tar.gz&nbsp;(722.6 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.04.F-Scan.ox1r_antagonist.tar.gz&nbsp;(549.4 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.05.F-Scan.ox2r_antagonist.tar.gz (768.4 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.06.F-Scan.KAT6A.tar.gz&nbsp;(407.9 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.07.F-Scan.PDE1B.tar.gz&nbsp;(470.7 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.08.F-Scan.Akt1_kinase.tar.gz&nbsp;(390.6 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.09.Cl-Scan.PPAR_Gama.tar.gz&nbsp;(412.9 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.10.Cl-Scan.erk12.tar.gz&nbsp;(352.4 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.11.Cl-Scan.KAT6A.tar.gz&nbsp;(408.2 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.12.Br-Scan.PRMT4.tar.gz&nbsp;(522.1 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.13.Me-Scan.BD1_scaffold_thiophene.tar.gz&nbsp;(187.6 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.14.Me-Scan.BD1_scaffold_furan.tar.gz&nbsp;(187.3 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.15.Me-Scan.HIV-1.tar.gz&nbsp;(740.2 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.16.Me-Scan.PPAR_Gama.tar.gz&nbsp;(412.8 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.17.Me-Scan.avb6.tar.gz&nbsp;(2.2 GB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.18.MeO-Scan.KAT6A.tar.gz&nbsp;(409.3 MB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.19.MeO-Scan.ox2r_agonist.tar.gz&nbsp;(1.1 GB)</strong></li> <li><strong>AMBER-GPUTI_PAS_input.20.HO-Scan.ox2r_agonist.tar.gz&nbsp;(1.1 GB)</strong><br> &nbsp;</li> </ul> </li> <li><strong>Data Structures inside each files:</strong> <ul> <li><strong>directory_tree.20_PDB_66_MOL2_input_coordinates_for_PAS.txt&nbsp;(5 kB)</strong></li> <li><strong>directory_tree.AMBER18.GPUTI.scripts.txt&nbsp;(91 kB)</strong></li> <li><strong>directory_tree.AMBER18_input_for_PAS_GPUTI_simulations.txt&nbsp;(1.5 MB)</strong></li> </ul> </li> </ul>