Modules configuration

It should be noted that in all cases the project directory (dir=) and project name (project=) must be declared in the main auto-p2docking config file.

Ligand selection

evoppi_querier

This module allows you to retrieve GeneID lists from the EvoPPI databases (http://evoppi.i3s.up.pt). It takes as input a GeneID and returns from EvoPPI the corresponding list(s) of interactors, as text files with one GeneID per line. The following parameters must be declared, one per line, in a config file, which must be in the input folder of the module:

  • evoppi_q_species=
  • evoppi_q_geneid=
  • evoppi_q_level=
  • evoppi_q_intdb=
  • evoppi_q_intmod=
  • evoppi_q_intpolyq=
  • evoppi_q_preddb=
  • evoppi_q_predmod=
  • evoppi_q_predpolyq=
  • evoppi_q_max_int=

where:

  • evoppi_q_species indicates the name of the species of interest, for instance “Homo sapiens”. The full list of available species can be found in the evoppi_querier_options section.
  • evoppi_q_geneid indicates the GeneID for the gene that encodes the protein to be studied.
  • evoppi_q_level specifies the interaction level (which is the degree of distance (up to a maximum of three) to retrieve transitive interactions).
  • evoppi_q_intdb indicates the name of the interactome databases to be analyzed. The full list of available databases can be found in the evoppi_querier_options section. If more than one database is to be analyzed, their names must be separated by semicolons (for instance, “BioGRID; HIPPIE; Mentha; Mint;Pina2”). * means all databases.
  • evoppi_q_intmod indicates the name of the Modifiers interactome databases to be analysed. The full list of available databases can be found in the evoppi_querier_options section. If more than one database is to be analyzed, their names must be separated by semicolons. * means all databases.
  • evoppi_q_intpolyq indicates the name of the PolyQ interactome databases to be analyzed. The full list of available databases can be found in the evoppi_querier_options section. If more than one database is to be analyzed, their names must be separated by semicolons. * means all databases.
  • evoppi_q_preddb indicates the name of the predictomes (predict interactome) databases to be analyzed. The full list of available databases can be found in the evoppi_querier_options section. If more than one database is to be analyzed, their names must be separated by semicolons. * means all databases.
  • evoppi_q_predmod indicates the name of the Modifiers predictomes databases to be analyzed. The full list of available databases can be found in the evoppi_querier_options section. If more than one database is to be analyzed, their names must be separated by semicolons. * means all databases.
  • evoppi_q_predpolyq indicates the name of the PolyQ predictomes databases to be analyzed. The full list of available databases can be found in the evoppi_querier_options section. If more than one database is to be analyzed, their names must be separated by semicolons. * means all databases.
  • evoppi_q_max_int Indicates the maximum number of interactions to be analyzed (a random sample taken from the full list of interactions).

Note 1: all parameters are mandatory, otherwise the program will not run. evoppi_q_int.* and evoppi_q_pred.* can be empty, but at least one interactome/predictome name must be specified. Note 2: the output folder of EvoPPi accepts up to two output files.

geneid2uniprotkb

This module allows getting the reference UniProtKB number associated with a given GeneID. It accepts a list of Gene IDs, one per line, and returns a list of UniprotKB numbers from NCBI gene (https://www.ncbi.nlm.nih.gov/gene), one per line. The input file must have the .gi extension.

intersect

This module allows you to get the intersection of two or more UniProtKB or GeneID lists. It generates a list of all UniProtKBs or GeneIDs common to all files.

exclude

This module allows you, given two lists of two UniProtKBs/GeneIDs, to get one list with all UniProtKBs/GeneIDs present in the larger list that are not present in the smaller list.

copy

This module copies all files from one folder to another. It should be noted that for the pipeline to work, the PDB files of all ligands must be in a folder named Ligands, and the PDB files of the receptor in a folder named Receptor, both under a folder called PDBs, under the project folder (the variable project is assigned in the config file). Therefore, if this is the intended operation, in the pipeline file, it should be declared on two different lines “copy name_of_ligand_input_folder PDBs/Ligands”, and “copy name_of_receptor_input_folder PDBs/Receptor”.

human_prot_atlas

This module allows retrieving lists of proteins encoded by genes expressed in a given tissue. It accepts as input a list with UniProtKb numbers, one per line, and returns a list of UniProtKb numbers, one per line, of those genes that are expressed in the specified tissue. In the auto-p2docking configuration file, there are three parameters to be specified (one per line), namely: h_prot_atlas_inc=, h_prot_atlas_mode=, and h_prot_atlas_exc=

  • h_prot_atlas_inc: list of tissues to be considered, separated by ;, or * to analyse all available tissues (that is used by default). For instance, h_prot_atlas_inc=”Brain_cerebral_cortex; Brain_hippocampal_formation”. The list of available tissues are: Brain_cerebral_cortex, Brain_hippocampal_formation,

Brain_amygdala, Brain_basal_ganglia, Brain_thalamus, Brain_hypothalamus, Brain_midbrain, Brain_cerebellum, Brain_pons, Brain_medulla_oblongata, Brain_spinal_cord, Brain_white_matter, Choroid_plexus, Salivary_gland, Esophagus, Tongue, Stomach, Intestine, Pancreas, Kidney, Urinary_bladder, Breast, Vagina, Cervix, Endometrium, Fallopian_tube, Ovary, Placenta, Skin, Adipose_tissue, Seminal_vesicles, Prostate, Epididymis, Testis, Gallbladder, Liver, Lymphoid_tissue, Bone_marrow, Lung, Pituitary_gland, Thyroid_gland, Parathyroid_gland, Adrenal_gland, Smooth_muscle, Heart, Retina.

  • h_prot_atlas_mode: you can select all proteins by writing union or only those

that are present in all selected tissues if you write intersection . If you do not provide information in this field, union is used by default.

  • h_prot_atlas_exc: If h_prot_atlas_inc=* has been declared, you can exclude specific tissue(s) by indicating their name(s), separated by ;.