Available Tools

Listed below are the tools made available through the PLEX client.

Tool	Category	Description	Example Command
Equibind	Small Molecule Binding	Docking of small molecules to a protein	./plex create -t tools/equibind.json -i testdata/binding/abl --autoRun=true
Diffdock	Small Molecule Binding	Docking of small molecules to a protein	./plex create -t tools/diffdock.json -i testdata/binding/abl --autoRun=true
RF Diffusion	Protein Design	Design protein binders; generally useful for conditional generation of protein backbones	./plex create -t tools/rfdiffusion.json -i testdata/design --autoRun=true
Colabfold	Protein Folding	Protein folding prediction	./plex create -t tools/colabfold-mini.json -i testdata/folding --autoRun=true
ODDT	Small Molecule Binding	Scoring of protein-ligand complexes	./plex create -t tools/oddt.json -i testdata/scoring/abl --autoRun=true
bam2fastq		Sort BAM by qname and Extract Fasta reads R1 R2 with RG using samtools

If there are any additional tools you would like made available in the PLEX client, please see how to contribute a tool.