Ligand binding affinity prediction with PRODIGY-lig

Submodules

haddock.modules.scoring.prodigyligand.prodigylig module

Module contents

PRODIGY-ligand scoring module.

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

class haddock.modules.scoring.prodigyligand.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/prodigyligand/defaults.yaml'))[source]

Bases: ScoringModule

HADDOCK3 module to perform energy minimization scoring.

classmethod confirm_installation() → None[source]: Confirm module is installed.

name: str = 'prodigyligand'

Default Parameters

Easy

ligand_chain

default: ‘B’
type: string
title: Chain ID of the ligand.
short description: Chain ID of the ligand.
long description: Chain of the ligand to score. Used to know in which chain the ligand is found.
group: scoring
explevel: easy

ligand_resname

default: ‘UNK’
type: string
title: Residue name of the ligand.
short description: Residue name of the ligand.
long description: Residue name of the ligand to score. Must be present in the ligand chain.
group: scoring
explevel: easy

receptor_chain

default: ‘A’
type: string
title: Chain ID of the receptor.
short description: Chain ID of the receptor.
long description: Chain ID of the receptor. Used to know what chain should be considered as receptor interacting with the ligand.
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

distance_cutoff

default: 10.5
type: float
title: Distance cutoff (Å) to extract amino-acids from the receptor.
min: 1.0
max: 100.0
short description: Distance cutoff (Å) to extract amino-acids from the receptor.
long description: Distance cutoff (Å) to extract amino-acids from the receptor in contact with the ligand.
group: scoring
explevel: expert

electrostatics

default: True
type: boolean
title: Use the electrostatic component.
short description: Use the electrostatic component from the input model to make the prediction.
long description: Use the electrostatic component from the input model to make the prediction, if available. The electroststics must have been computed by HADDOCK and written in the REMARK of the model.
group: scoring
explevel: expert