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