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 "In silico Positional Analogue Scanning with Amber GPU-TI, J. Chem. Inf. Model. 2022, 62, 18, 4448–4459".

https://doi.org/10.1021/acs.jcim.2c00860

The repository contains the following data:

20_PDB_66_MOL2_input_coordinates_for_PAS.tar.gz (7.7MB)

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.

AMBER18.GPUTI.scripts.tar.gz (597.2 M)

Scripts and example of CDK8 TI output for GPU TI ddG calculation and cycle closure correlation.

Supporting_Information_Tables_dG_ddG_small_big_change.xlsx (60kB)

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)

AMBER-GPUTI_PAS_input.01.N-Scan.CDK8.tar.gz (736.2MB)

AMBER-GPUTI_PAS_input.02.N-Scan.Tankyrase.tar.gz (266.1 MB)

AMBER-GPUTI_PAS_input.03.N-Scan.HCV_NS5B_gt1b.tar.gz (722.6 MB)

AMBER-GPUTI_PAS_input.04.F-Scan.ox1r_antagonist.tar.gz (549.4 MB)

AMBER-GPUTI_PAS_input.05.F-Scan.ox2r_antagonist.tar.gz (768.4 MB)

AMBER-GPUTI_PAS_input.06.F-Scan.KAT6A.tar.gz (407.9 MB)

AMBER-GPUTI_PAS_input.07.F-Scan.PDE1B.tar.gz (470.7 MB)

AMBER-GPUTI_PAS_input.08.F-Scan.Akt1_kinase.tar.gz (390.6 MB)

AMBER-GPUTI_PAS_input.09.Cl-Scan.PPAR_Gama.tar.gz (412.9 MB)

AMBER-GPUTI_PAS_input.10.Cl-Scan.erk12.tar.gz (352.4 MB)

AMBER-GPUTI_PAS_input.11.Cl-Scan.KAT6A.tar.gz (408.2 MB)

AMBER-GPUTI_PAS_input.12.Br-Scan.PRMT4.tar.gz (522.1 MB)

AMBER-GPUTI_PAS_input.13.Me-Scan.BD1_scaffold_thiophene.tar.gz (187.6 MB)

AMBER-GPUTI_PAS_input.14.Me-Scan.BD1_scaffold_furan.tar.gz (187.3 MB)

AMBER-GPUTI_PAS_input.15.Me-Scan.HIV-1.tar.gz (740.2 MB)

AMBER-GPUTI_PAS_input.16.Me-Scan.PPAR_Gama.tar.gz (412.8 MB)

AMBER-GPUTI_PAS_input.17.Me-Scan.avb6.tar.gz (2.2 GB)

AMBER-GPUTI_PAS_input.18.MeO-Scan.KAT6A.tar.gz (409.3 MB)

AMBER-GPUTI_PAS_input.19.MeO-Scan.ox2r_agonist.tar.gz (1.1 GB)

AMBER-GPUTI_PAS_input.20.HO-Scan.ox2r_agonist.tar.gz (1.1 GB)

Data Structures inside each files:

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)