WaSiMap - Test Data

WaSiMAP - MD Test Data This repository contains the MD test data for the WaSiMap (Water Site Mining and Analysis Pipeline) software, consisting of two datasets. Dataset I has three MD simulations of the ABL1-SH3 in complex with WT peptide 3bp-1, and also with peptide variants p3 and p4. Two such simulations are in H5 format (sim1 and sim2), and the remaining simulation (sim3) in .NC format, with its corresponding Amber topology file in PRMTOP format. The simulation "sim1" contains the wild-type complex, whereas "sim2" and "sim3" contain the variants (p3 and p4). These files can be downloaded manually by the end-user and deposited in a folder, or automatically using the wasimap CLI command with the flag --testdata The simulation time is 2ns in 1000 frames (2ps samples) All simulations contain explicit TIP3P water The total size of all files is 320MB The purpose of these simulations is to serve as example to showcase the cappabilities of WaSiMAP in exctracting and visualizing water-site information. Dataset II contains additional MD simulations of the ABL1-SH3 in complex with WT peptide 3bp-1, and also with the high-affinity variant p41. Each complex was simulated in triplicate for 50 ns, in addition to one 500 ns simulation. The purpose of this dataset was to assess reproducibility, consistency and performance of the tool handling longer MD simulations, and replicas of the same system. Archived folder "S2 Data.zip" contains the templates, MD input files, scripts and settings that were used to run the MD simulations with OpenMM. For further details on how these simulations were created, refer to the supplementary data S2 Appendix of the WaSiMAP manuscript.