Binding affinity prediction with PRODIGY

Submodules

Module contents

PRODIGY protein complex scoring module

This module performs the scoring of input complexes using PRODIGY (protein). It predicts deltaG of the complex and can return predictions as either deltaG or pKd values.

Note that PRODIGY-protein is limited to natural amino-acids.

class haddock.modules.scoring.prodigyprotein.HaddockModule(order: int, path: Path, initial_params: str | Path = PosixPath('/opt/hostedtoolcache/Python/3.10.17/x64/lib/python3.10/site-packages/haddock/modules/scoring/prodigyprotein/defaults.yaml'))[source]

Bases: ScoringModule

HADDOCK3 module to perform energy minimization scoring.

classmethod confirm_installation() → None[source]

Confirm module is installed.

name: str = 'prodigyprotein'

Default Parameters

Easy

chains

default: []
type: list
title: Chains to be scored.
short description: List of chains to be scored. If empty/unspecified, all inter-chains contacts will be considered for the final prediction.
long description: List of chains to be scored. If empty/unspecified, all inter-chains contacts will be considered for the final prediction. In specific cases, for example antibody-antigen complexes, some chains should be considered as a single molecule. Use the chains parameter to provide a list of chains that should be considered for the calculation. Use commas to include multiple chains as part of a single group. [“A”, “B”] => Contacts calculated (only) between chains A and B. [“A,B”, “C”] => Contacts calculated (only) between chains A and C; and B and C. [“A”, “B”, “C”] => Contacts calculated (only) between chains A and B; B and C; and A and C.
group: scoring
explevel: easy

temperature

default: 25.0
type: float
title: Temperature (°C) at which to perform the conversion to pKd.
min: -273.15
max: 95.0
short description: Temperature (°C) at which to perform the conversion from deltaG (kcal.mol-1) to pKd.
long description: Temperature (°C) at which to perform the conversion from deltaG (kcal.mol-1) to pKd.
group: conversion
explevel: easy

to_pkd

default: True
type: boolean
title: Converts binding affinity values to pKd.
short description: Converts binding affinity values to pKd.
long description: By default, prodigy-lig results in deltaG (kcal.mol-1), but this parameter allows to convert results to pKd.
group: conversion
explevel: easy

Expert

accessibility_cutoff

default: 0.05
type: float
title: Accessibility threshold for BSA analysis.
min: 0.0
max: 1.0
short description: Accessibility threshold for BSA analysis.
long description: Accessibility threshold for BSA analysis.
group: scoring
explevel: expert

distance_cutoff

default: 5.5
type: float
title: Distance cutoff (Å) to extract amino-acids in contact between the two chains.
min: 1.0
max: 100.0
short description: Distance cutoff (Å) to extract amino-acids in contact between the two chains.
long description: Distance cutoff (Å) to extract amino-acids in contact between the two chains.
group: scoring
explevel: expert