Import Antibody FASTA Files¶
Category Paths
Follow one of these paths in the Orion user interface, to find the floe.
Product-based/AbXtract
Role-based/Computational Chemist
Role-based/Bioinformatician
Solution-based/Virtual-screening/DB Preparation
Solution-based/Biologics/Antibody Design
Description
In this floe, input FASTA files of antibody sequences will be put into a dataset with records containing antibody H and L sequences and the antibody name/identifier. Because multiple antibody systems are allowed in a single FASTA file, the sequence titles are used to link the Fv chains. The identifying H and L chain IDs must also be present in the sequence title. See the Input FASTA File parameter for more detail on proper formatting.
Related Floes: Antibody Sequences to 3D Models Floe
Promoted Parameters
Title in user interface (promoted name)
Inputs
Input FASTA File (fasta_files): Input FASTA Files containing sequence information. Multiple protein systems are allowed, and all input sequences must follow appropriate formatting. Sequence titles are used to match multiple sequences in the same protein system. The format for sequence titles start with a unique protein name followed by an underscore and the chain ID (e.g., >Gag-Pol Polyprotein_C defines Name=Gag-Pol Polyprotein, Chain=C). Antibodies must further define each system’s H and L chains. Any chain IDs other than H/L incomplete systems, or duplicate entries will fail all sequences for that antibody system.
Required
Type: file_in
VH Sequence Field (vh_seq): The heavy chain sequences from the FASTA file will save sequence data to this field.
Required
Type: field_parameter::string
Default: VH
VL Sequence Field (vl_seq): The light chain sequences from the FASTA file will save sequence data to this field.
Required
Type: field_parameter::string
Default: VL
Outputs
Output dataset of imported sequences (out): Imported sequences in a dataset ready for sequence 2 model floe
Required
Type: dataset_out
Default: Antibody_Sequences
Failed Sequence Output (failed_out): Any sequences that cannot adhere to the selected sequence numbering scheme will fail.
Required
Type: dataset_out
Default: failed_Antibody_Sequences