Liability Quantification Across CDRs - AbXtract

Quantify sequence-based liabilities across all CDRs.

Promoted Parameters

  • Select All Datasets to Quantify Liabilities (data_source) : Input all the datasets (may be multiple) to tabulate liabilities.
  • Biophysical Liabilities (string) : Net charge or hydropathy liabilities to quantify.
    Default: [‘Charge (>1)’]
    Choices: Charge (>-1), Charge (>0), Charge (>1), Charge (>2), Charge (>3), Charge (>4), Parker Hydropathy (<0.0), Parker Hydropathy (<-0.1), Parker Hydropathy (<-0.2), Parker Hydropathy (<-0.3), Parker Hydropathy (<-0.4), Parker Hydropathy (<-0.5), Parker Hydropathy (<-0.6), Parker Hydropathy (<-0.7), Parker Hydropathy (<-0.8), Parker Hydropathy (<-0.9), Parker Hydropathy (<-1.0), Parker Hydropathy (<-2.0), Parker Hydropathy (<-3.0), Parker Hydropathy (<-4.0), Parker Hydropathy (<-5.0)
  • Glycosylation Liabilities (string) : glycosylation liabilities to quantify.
    Default: [‘NXT/S - Glycosylation’]
    Choices: NXT/S - Glycosylation, NXT - Glycosylation. NXS - Glycosylation
  • Cysteine Liabilities (string) : cysteine-based liabilities to quantify.
    Default: [‘Unpaired Cysteine’]
    Choices: Unpaired Cysteine, Any Cysteine
  • Deamidation Liabilities (string) : deamidation liabilities to quantify.
    Default: [‘NG - Deamidation’, ‘NS - Deamidation’, ‘NT - Deamidation’, ‘NN - Deamidation’, ‘GNF - Deamidation’, ‘GNY - Deamidation’, ‘GNT - Deamidation’, ‘GNG - Deamidation’, ‘QG - Glutamine Deamidation’]
    Choices: N[GSTN] - Deamidation, NG - Deamidation, NS - Deamidation, NT - Deamidation, NN - Deamidation, GN[FYTG] - Deamidation, GNF - Deamidation, GNY - Deamidation, GNT - Deamidation, GNG - Deamidation, QG - Glutamine Deamidation
  • Hydrolysis Liabilities (string) : hydrolysis liabilities to quantify.
    Default: [‘DP - Hydrolysis’]
    Choices: DP - Hydrolysis
  • Isomerization Liabilities (string) : isomerization liabilities to quantify.
    Default: [‘DG - Isomerization’, ‘DS - Isomerization’, ‘DD - Isomerization’]
    Choices: D[GSD] - Isomerization, DG - Isomerization, DS - Isomerization, DD - Isomerization
  • Polyspecificity Liabilities (string) : polyspecificity liabilities to quantify.
    Default: [‘Three Consecutive Aromatics - Polyspecificity’, ‘RR - Polyspecificity’, ‘VG - Polyspecificity’, ‘VV - Polyspecificity’, ‘WW - Polyspecificity’, ‘GGG - Polyspecificity’, ‘WXW - Polyspecificity’, ‘YY - Polyspecificity’]
    Choices: Three Consecutive Aromatics - Polyspecificity, RR - Polyspecificity, VG - Polyspecificity, VV - Polyspecificity, YY - Polyspecificity, WW - Polyspecificity, GGG - Polyspecificity, WXW - Polyspecificity
  • Keep Only Functional Sequences (boolean) : Eliminates non-functional sequences, truncations, stop-codons, frame-shifts.
    Default: True
  • Output Name of Dataset with Quantified Liabilities (dataset_out) : Dataset of sequences with quantified liabilities.
    Default: liabilities_quantified.
  • Failed Dataset Output Name (dataset_out) : Contains failed records from both upstream and downstream processes.
    Default: problematic.
Hidden Parameters
  • Liability Database File (file_in) : Provide liabilities file (xls, csv, tsv) with 2 columns (regex pattern, name of liability). DO NOT INCLUDE characters ‘+’ or ‘,’ in second description ‘name of liability’ column. Special case liabilities include net charge, Parker hydropathy and unpaired cysteine. For net charge, write “Charge”, case-sensitive, in first column and the net charge integer in second column (values above are flagged). Similarly, for Parker hydropathy, write “Parker Hydropathy”, case-sensitive, in first column and the hydropathy float value in second column (values below are flagged). For unpaired cysteine write “Cysteine”, case-sensitive, and in second column can write anything but typically write “Unpaired Cysteine”. NOTE, if even number of cysteines exists and cysteines are only spaced within 3 AAs, these are still considered unpaired.