Hi everyone,

I wanted to share ProteinIQ, a bioinformatics platform I started after finishing my PhD in bioinformatics.

Disclosure: I am the founder.

During my PhD, one thing kept bothering me: many useful analyses were blocked less by the science and more by the setup. A tool might require the right environment, GPU access, fragile dependencies, file conversions, output parsing, and a way to keep results organized. That friction made routine analyses harder for wet-lab collaborators and students, and it also wasted time for bioinformaticians who already knew what needed to be run.

ProteinIQ is my attempt to remove that setup layer while keeping the scientific tools visible and faithful to their expected behavior.

Link: ProteinIQ.io Contact: support@proteiniq.io

What it does

ProteinIQ lets you run hosted bioinformatics tools from the browser for protein folding, docking, design, sequence analysis, RNA/DNA utilities, ligand analysis, molecular dynamics, and structure analysis.

It includes tools such as AlphaFold2, ESMFold, Boltz-2, Chai-1, Protenix, AutoDock Vina, GNINA, SMINA, MAFFT, Clustal Omega, HMMER, FoldSeek, ViennaRNA, ProteinMPNN, LigandMPNN, GROMACS, and others.

How a run works

• Choose a tool or start from a workflow
• Upload or paste sequences, structures, ligands, or other supported inputs
• Adjust settings where needed
• Run the analysis on hosted compute or in the browser, depending on the tool
• Get results with downloadable files, settings, job history, and outputs such as structures, scores, alignments, tables, and confidence metrics

Why I built it

I do not think every researcher should have to become a sysadmin before running a standard analysis. I also do not think code-free should mean black-box. The goal is to make common computational biology workflows easier to run while still returning the real scientific outputs that can be inspected, downloaded, and reused elsewhere.

Who it is for

ProteinIQ is meant for wet-lab scientists, students, clinicians, and biotech teams who need to run analyses without setting up local infrastructure. It is also useful for bioinformaticians who want a convenient place to run routine jobs, share results, or connect tools into reusable workflows.

I would be very interested in feedback from the Biostars community, especially:

• Missing tools you would expect to see
• Workflows that are still painful to run
• Output formats or provenance details that would make results easier to trust
• Places where a tool should preserve more of the original command-line behavior

Happy to answer questions here.