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 -tool equibind -input-dir testdata/binding/abl |
| Diffdock | Small Molecule Binding | Docking of small molecules to a protein | ./plex -tool diffdock -input-dir testdata/binding/abl |
| RF Diffusion | Protein Design | Design protein binders; generally useful for conditional generation of protein backbones | ./plex -tool rfdiffusion -input-dir testdata/design |
| Colabfold | Protein Folding | Protein folding prediction | ./plex -tool colabfold-mini -input-dir testdata/folding |
| ODDT | Small Molecule Binding | Scoring of protein-ligand complexes | ./plex -tool oddt -input-dir testdata/scoring/abl |
| 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.