Supporting data for "How many crystal structures do you need to trust your docking results?"
Year: 2025
Type: dataset
Abstract: # Files for the paper _"How many crystal structures do you need to trust your docking results?"_```@article{payne_how_2025, title = {How many crystal structures do you need to trust your docking results?}, url = {https://www.biorxiv.org/content/early/2025/09/24/2025.09.19.677428}, doi = {10.1101/2025.09.19.677428}, journal = {bioRxiv}, publisher = {Cold Spring Harbor Laboratory}, author = {Payne, Alexander Matthew and Kaminow, Benjamin and MacDermott-Opeskin, Hugo and Pulido, Iván and Scheen, Jenke and Castellanos, Maria A and Fearon, Daren and Chodera, John D. and Singh, Sukrit}, year = {2025}, note = {\_eprint: https://www.biorxiv.org/content/early/2025/09/24/2025.09.19.677428.full.pdf},}```# OrganizationZipped files are broken down below. All sizes are pre-zipped so you know how much the unzipped files will take up.## Input Data`input_data.tar.gz`| index | directory | size | description ||-------|------------------------------------------------|--------|------------------------------------------------------------------------------|| 1 | mpro_fragalysis-04-01-24_curated | 572 Mb | COVID Moonshot Fragalysis download with only the P- and S- series structures || 2 | mpro_fragalysis-04-01-24_curated_cache | 1.6 Gb | `1` prepared for docking with OpenEye || 3 | mpro_fragalysis-04-01-24_curated_cache_fixed | 1.2 Gb | `2` with ligand duplicates removed |## Input Data Analysis`input_data_analysis.tar.gz`This zipped folder contains the data derivable from the inputs used to analyze the docking results.| index | directory | size | description ||-------|--------------------------|--------|-------------------------------------------------------------------------------------|| 4 | chemical_similarity_data | 205 Mb | Pairwise ligand similarities calculated from the dataset in `3` || 5 | cmpd_date_dict | 628 Kb | Contains dictionary mappings of date to structure and structure to compound for `3` || 6 | ligand_files | 8.9 Mb | Ligands pulled from `3` into their own SDF files with accompanying metadata || 7 | protein_rmsd_data | 38 Mb | Protein-only RMSD comparisons from the crystal structures in `3` |## Raw Docking Results Four gzip-compressed tar files for each set of docking results.Each tar file containes a folder for each Query Ligand (represented by a number) with poses for each Reference Structure combined into a single multi-ligand SDF file.| index | file | size | description ||-------|----------------------|--------|-----------------------------------------------------------|| 8 | ALL_1_poses.tar.gz | 1.3 Gb | Full POSIT cross docking results with only 1 pose kept || 9 | FRED_1_poses.tar.gz | 1.3 Gb | FRED-only cross docking results with only 1 pose kept || 10 | ALL_50_poses.tar.gz | 20 Gb | Full POSIT cross docking results with up to 50 poses kept || 11 | FRED_50_poses.tar.gz | 37 Gb | FRED-only cross docking results with up to 50 poses kept |## Analyzed Data`analyzed_data.tar.gz`| index | folder | size | description ||-------|--------------------------|--------|----------------------------------------------------------------------------------------------------------------------------------------------|| 12 | config_files | 148 Kb | YAML files for storing settings for the various analyzes run with `harbor` || 13 | docked_ligand_rmsds | 398 Mb | Calculated RMSDs for posed ligands vs their crystal structure pose || 14 | combined_docking_results | 256 Mb | Contains the analyzed data in `json` and `parquet` form absent structural coordinates and with all the metadata gathered from `4-7` and `13` || 15 | analyzed_results | 334 Mb | Contains results of calculations on `14` used to generate paper figures |
Language: English
Subfield: Drug Discovery
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7213584498