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21 décembre 2023
- doi: 10.57745/GXZHH8
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Computer and Information Science Medicine, Health and Life Sciences HLA Antigens Molecular Dynamics Simulation B-cell epitope predictor Machine LearningCiter ce document
Diego AMAYA RAMIREZ et al., « MD simulations and ML dataset of HLA-EpiCheck epitope predictor tool », Recherche Data Gouv, ID : 10.57745/GXZHH8
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This dataset contains all the data used to implement the B-cell epitope predictor tool called HLA-EpiCheck (see https://doi.org/10.1101/2023.12.18.572133). CONTENTS: - pre-patches: Directory containing the computed pre-patches. A pre-patch corresponds to the set of residues within a given distance from a residue. The patches are generated subsequently by keeping only the solvent-accessible residues. Files are organized by locus and by antigen. A file contains the pre-patches associated to a given residue computed for any frame considered in the trajectory. + _patches_resid__size_.txt: Each line in the file corresponds to a pre-patch of a given frame. Line format : : Residue numbering is the same as in the PDB files. - trajectories: Directory contaning the MD data. Files are organized by locus and by antigen. + .dcd: 10ns MD trajectory comprising 1000 frames. Water molecules were removed. + .psf: Topology file of the .dcd trajectory. + .pdb: Starting structure of the MD simulation. - training_set_size_15.csv: training set used to train HLA-EpiCheck. - test_set_size_15.csv: test set used to evaluate HLA-EpiCheck. - table_patch_ID_antigen_residue.csv: Table containing the antigen and central residue associated to each patch. - model_ERF_radius_15.pkl: ML model of HLA-Epicheck in pickle format. Pickle version 4.0 used. - descriptors_eplets_non-confirmed.csv: Descriptors of the non-confirmed residue patches. - preds_non_confirmed_DQ.csv: HLA-EpiCheck predictions on the non-confirmed residue patches of eplets from locus DQ. - PDB_modeled_structures.txt : List of antigens modeled from a PDB structure with the corresponding PDB entry.