Surface extraction

pisa_ccp4_extract

This module takes as input the .pdb files of protein complexes obtained with the selected docking methodology and returns a .tsv file of the best protein complex (highest number of interacting residues) and the corresponding .pdb file of the best complex, using PDBePISA as implemented in the CCP4 (https://www.ccp4.ac.uk/) software. File names must be in the format ReceptorUniProtKB_database_LigandUniProtKB_database_DockingMethod_name_ComplexName (for instance, P15848_AF_P59665_ditasser_FTDOCK_56.pdb). The files must be placed in a folder named LigandUniProtKB_database (for instance, P59665_ditasser) within the module input folder.

pisa_server_extract

This module takes as input the .pdb files of protein complexes obtained with the selected docking methodology and returns a .tsv file of the best protein complex (highest number of interacting residues) and the corresponding .pdb file of the best complex, using the on-line PDBePISA (https://www.ebi.ac.uk/pdbe/pisa/) website. File names must be in the format ReceptorUniProtKB_database_LigandUniProtKB_database_DockingMethod_name_ComplexName (for instance, P15848_AF_P59665_ditasser_FTDOCK_56.pdb). The files must be placed in a folder named LigandUniProtKB_database (for instance, P59665_ditasser) within the module input folder.

pisa_xml_extract

This module takes as input one or more xml files of protein complexes generated by the PDBePISA server (https://www.ebi.ac.uk/pdbe/pisa/) and returns a summary (.tsv file) of the best protein complex (highest number of interacting residues). To use this utility with more than one protein pair, please create a main input folder and create as many folders inside it as there are protein pairs to be analyzed. The name of each folder should follow the structure: LigandUniProtKB_database (for instance, P59665_ditasser). Each folder should contain one or more PISAePDB xml files. This module should only be used, if you have XML files from the PDBePISA server.