Today we are opening Workflows to the public. Workflows let you connect ProteinIQ tools into reusable bioinformatics pipelines, run the full analysis from one canvas, and inspect each step without moving files between separate tool pages.
Most computational biology work is not a single job. You clean a structure before docking. You filter a ligand library before scoring. You predict a model, validate it, and then decide whether it is good enough for the next step. Workflows are built for that middle layer: the repeated handoff between tools where a lot of real project time disappears.
Build pipelines from real ProteinIQ tools
The workflow editor uses the same scientific tools already available in ProteinIQ. You can add data nodes for proteins, structures, DNA, RNA, molecules, and text inputs, then connect them to compatible analysis tools.
The editor understands tool inputs and outputs, so connections are typed around scientific artifacts instead of arbitrary files. Multi-input tools can route structures, ligands, sequences, and other inputs into the correct ports, and combination modes let you control whether a run uses every pair, paired inputs, or the first item only.
You can start from a blank canvas or use a template from the workflow template library. The initial public templates cover virtual screening, structure prediction and validation, sequence alignment and phylogeny, antibody developability, RNA analysis, protein design, docking, ADMET triage, and batch structure preparation.
Add filters, breakpoints, and review steps
Workflows are not just a way to queue jobs. They include controls for deciding what moves forward.
Tool-node filters can pass only the rows or molecules that match a condition, such as keeping compounds that pass a PAINS filter before sending them into docking. Breakpoints let a workflow pause at selected nodes so you can review intermediate results before continuing.
That matters for expensive or judgment-heavy pipelines. You can stop after target preparation, inspect a predicted structure before downstream validation, or narrow a ligand set before launching a larger docking or free-energy step.
See cost and run state before the work starts
The editor estimates workflow credit cost before execution. For pipelines where filters change how many downstream jobs will run, the estimate can show a range.
When a workflow starts, ProteinIQ reserves the maximum estimated credits up front and refunds unused credits after completion. Runs report node-level progress, queued and running jobs, completed outputs, partial failures, and final results. You can open individual node results or download workflow outputs together.
Workflows can be saved, duplicated, exported, imported, and rerun. That makes them useful not only for one analysis, but for repeated screens, team handoffs, and method records you want to keep alongside the results.
How to try workflows
Open Workflows from the app sidebar, create a blank workflow, or start from Templates. Running workflows is available on Plus, Pro, and Enterprise plans. Grandfathered Lite subscribers also retain workflow access; see Pricing for the current plan comparison.
This first public release focuses on making multi-step analysis easier to build, run, and review. We will keep expanding the set of workflow-ready tools and templates as more ProteinIQ tools support workflow-safe inputs and outputs.
Founder and computational chemist, ProteinIQ
Dr. Matic Broz is the founder of ProteinIQ and a computational chemist. He completed a PhD focused on protein structure, molecular dynamics, and neural networks, and writes about structural biology and scientific software.