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Files for split_train, split_valid, and split_test arguments #36 Hi, I am running train py, and this line of code complains the input is a directory complex_names_all = read_strings_from_txt (self split_path) The original code snippet, read_strings_from_text needs a file def read_strings_from_txt (path
Output Files | luwei0917 DynamicBind | DeepWiki DynamicBind produces different types of output files depending on the operating mode (Dynamic Docking, High-Throughput Screening, or Animation Generation), providing both structural data and performance metrics for protein-ligand complexes For information about running DynamicBind to generate these outputs, see Basic Usage and Advanced Usage
GitHub - luwei0917 DynamicBind: repo for DynamicBind: Predicting ligand . . . Source code for the Nature Communications paper DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model DynamicBind recovers ligand-specific conformations from unbound protein structures (e g AF2-predicted structures), promoting efficient transitions between different equilibrium states
Usage Guide | luwei0917 DynamicBind | DeepWiki This guide provides step-by-step instructions for using DynamicBind to predict protein-ligand complex structures and generate binding animations It covers the essential workflows, command-line parame
deepchem examples binding_pockets binding_pocket_datasets. py . . . - GitHub Filter these manually missing_pdbs = ["1d2v", "1jou", "1s8j", "1cam", "4mlt", "4o7d"] contents = [] with open (labels_file) as f: for line in f: if line startswith ("#"): continue else: # Some of the ligand-names are of form (FMN ox)
PDBbind+ The primary objective of the PDBbind database is to offer a comprehensive collection of experimental binding affinity data for all biomolecular complexes recorded in the Protein Data Bank (PDB)