Docking

hdock

This module allows the use of HDOCK (see the hdock-builder Docker image at https://hub.docker.com/r/pegi3s/hdock-builder), a hybrid docking protocol that combines both template-based and template-free approaches. It takes two .pdb files as input and returns the .pdb of the 100 highest scoring docking protein complexes generated by HDOCK. The ligand and receptor .pdb files should have the following name structure: UniProtKB_database.pdb (for instance, P59665_AF.pdb, P15848_ditasser.pdb).The module expects the .pdb files of the corresponding proteins to be placed in the PDBs/Ligands and PDBs/Receptor folders. If more than one ligand .pdb file is present in the PDBs/Ligands folder, the module will proceed with the analysis of all possible receptor/lingand pairs.

haddock

This module allows the use of HADDOCK (see the haddock24-builder docker image at https://hub.docker.com/r/pegi3s/haddock24-builder), an information-driven flexible docking approach that accurately models the 3D structure of macromolecular complexes. It returns the PDBs of the docking protein complexes with a z-score less than or equal to 0. The complexes clusters resulting from all possible predicted dockings are scored based on a statistic called the z-score. The z-score represents how many standard deviations the HADDOCK score of a given cluster is from the mean of all clusters obtained, the lower the z-score, the better the predictions. If the user wants to see all the files created during the docking process he/she can set the parameter haddock_all_files to y, if the user only wants to see the most important files, he/she can set this parameter to n. The ligand and receptor PDB files should have the following name structure: UniProtKB_database (for instance, P15848_AF.pdb). It also uses the active and passive sites of each protein, which must have the following name structure: UniProtKB_database_active.sites and UniProtKB_database_passive.sites (for instance, P15848_AF_active.sites.csv, P15848_AF_passive.sites.csv). The active and passive sites must be placed in a folder named UniProtKB_database (for instance, P15848_AF) within the module’s input folder. The module expects the .pdb files of the corresponding proteins to be placed in the PDBs/Ligands and PDBs/Receptor folders.

pydock_ftdock

This module facilitates the use of the Ftdock software as implemented in the pydock software (see the pydock3-builder Docker image at https://hub.docker.com/r/pegi3s/pydock3-builder). It returns the PDBs of the docking protein complexes with the highest score. The parameter pydock_ftdock_number_of_solutions specifies the number of solutions to analyze, this number must be less than or equal to 10000 (recommended: 100). The parameter pydock_ftdock_best_pdb specifies the number of best solutions (recommended: 5). The .pdb files of the ligands and receptor, must have the following name structure: UniProtKB_database (for instance, P15848_AF.pdb). Ftdock also uses active and passive sites for each protein, which must have the following name structure: UniProtKB_database_active.sites and UniProtKB_database_passive.sites (for instance, P15848_AF_active.sites.csv, P15848_AF_passive.sites.csv). The active and passive sites must be placed in a folder named UniProtKB_database (for instance, P15848_AF) within the module’s input folder. The module expects the .pdb files of the corresponding proteins to be placed in the PDBs/Ligands and PDBs/Receptor folders.