schrodinger.application.bioluminate.tap_analysis module

Script to calculate the TAP descriptors for a given antibody sequence. The TAP descriptors are a set of five metrics proposed in the paper “Five computational developability guidelines for therapeutic antibody profiling” by Raybould et al., which are designed to predict the developability of therapeutic antibodies based on their sequence and structure.

From the TAP paper: M.I.J. Raybould, C. Marks, K. Krawczyk, B. Taddese, J. Nowak, A.P. Lewis, A. Bujotzek, J. Shi, & C.M. Deane, Five computational developability guidelines for therapeutic antibody profiling, Proc. Natl. Acad. Sci. U.S.A. 116 (10) 4025-4030, https://doi.org/10.1073/pnas.1810576116 (2019).

class schrodinger.application.bioluminate.tap_analysis.TapFeature

Bases: Enum

TotalCDRLength = 'Total CDR Length'
PSH = 'CDR Vicinity PSH Score'
PPC = 'CDR Vicinity PPC Score'
PNC = 'CDR Vicinity PNC Score'
SFvCSP = 'SFvCSP Score'
class schrodinger.application.bioluminate.tap_analysis.TapPatchContributions(psh, ppc, pnc)

Bases: NamedTuple

psh: float

Alias for field number 0

ppc: float

Alias for field number 1

pnc: float

Alias for field number 2

schrodinger.application.bioluminate.tap_analysis.calculate_tap_descriptors(heavy_seq: str, light_seq: str) → DataFrame

Calculate the TAP descriptors for a given heavy and light chain sequence.

Parameters:

  • heavy_seq – The amino acid sequence of the heavy chain.

  • light_seq – The amino acid sequence of the light chain.

Returns:

A DataFrame containing the TAP descriptors for the given sequences.

schrodinger.application.bioluminate.tap_analysis.calculate_tap_descriptors_from_structure(st: Structure) → DataFrame

Calculate TAP descriptors for an existing antibody structure.

The input structure is copied before annotation, so this function does not add TAP or IMGT annotation properties to the caller’s structure.

Parameters:

st – An antibody Fv or larger antibody structure.

Returns:

A DataFrame containing the TAP descriptors for the structure.

schrodinger.application.bioluminate.tap_analysis.calculate_total_cdr_length(heavy_seq: str, light_seq: str) → int

Calculate the total CDR length (using IMGT definition) for the given heavy and light chain sequences.

Parameters:

  • heavy_seq – The amino acid sequence of the heavy chain.

  • light_seq – The amino acid sequence of the light chain.

Returns:

The total CDR length.

schrodinger.application.bioluminate.tap_analysis.calculate_total_cdr_length_from_structure(st: Structure) → int

Calculate total IMGT CDR length from antibody region annotations.

Parameters:

st – An antibody structure annotated with TAP’s IMGT scheme.

Returns:

The number of residues annotated as H1-H3 or L1-L3.

schrodinger.application.bioluminate.tap_analysis.calculate_cdr_vicinity_patch_scores(st: Structure) → TapPatchContributions

Calculate all three CDR-vicinity patch scores in one pass.

schrodinger.application.bioluminate.tap_analysis.get_cdr_vicinity_patch_contributions(st: Structure) → Generator[TapPatchContributions, None, None]

Calculate PSH, PPC, and PNC contributions for each TAP surface patch.

schrodinger.application.bioluminate.tap_analysis.get_distance_sq(res1, res2) → float

Get the squared distance between two residues, defined as the minimum distance squared between any heavy atoms in the two residues.

Parameters:

  • res1 – The first residue.

  • res2 – The second residue.

Returns:

The shortest heavy-atom distance squared between the two residues.

schrodinger.application.bioluminate.tap_analysis.calculate_sfvcsp(st: Structure) → float

Calculate the SFvCSP score for the given structure.

Parameters:

st – an antibody Fv structure.

Returns:

The SFvCSP score.