quick-fold-nf

Overview

A Nextflow workflow for protein structure prediction.

Configuration

• inputFile: FASTA file with one or more sequences (required)
• resultsDir: directory where to store the results (default: results/yyyy.MM.dd-HH.mm.ss-quick-fold)
• esmfold.args: options passed to ESMFold (default: "--num-recycles 4 --chunk-size 16")
• openmm.pdb.relax.args: options passed to OpenMM PDB relaxation (default: "--fix-pdb")

Running the workflow

Install or update the workflow

nextflow pull stracquadaniolab/quick-fold-nf

Run the analysis

nextflow run stracquadaniolab/quick-fold-nf

Results

• $resultsDir/predicted/<seqid>.pdb: PDB file for each sequence in input as predicted by ESMFold.
• $resultsDir/relaxed/<seqid>.pdb: PDB files after energy minimization.

Authors

• Giovanni Stracquadanio