Start Guide

ProteinIQ helps researchers run bioinformatics analyses from the browser without setting up local software or compute infrastructure. This guide gets you from a new account to a completed result, with a few paths depending on what you need to do first.

Overview of ProteinIQ

Start here if you want to understand the layout and core workflows before running a job.

• Browse tools: View available analysis, folding, docking, design, screening, conversion, and utility tools
• Review your history: Reopen jobs, inspect statuses, and return to previous results in the active workspace
• Browse files: Upload files, save important job outputs, and organize reusable files into collections
• Check usage: Review your workspace credit balance and recent usage

Most work starts from a tool page. A tool page contains the input area, configuration controls, credit cost, submit action, and result view for that analysis.

Set up your workspace

ProteinIQ uses workspaces for credits, jobs, files, and collaboration. When you create an account, ProteinIQ creates a personal workspace named My Workspace and grants 100 promotional credits.

Create your account

1. Go to /sign-up
2. Create an account with the email you want to use for research work
3. Open /app after signup
4. Confirm that My Workspace is selected in the workspace dropdown (top-right)

Choose the right setup path

Individual researchers

• Use My Workspace for personal analyses, saved jobs, files, and credits
• Start with Protein Parameters or PDB to FASTA to learn the basic tool flow
• Review Credits before running heavier paid jobs

Teams and labs

• Use Workspaces and seats to understand shared credits, member access, and seat rules
• Use Pricing and billing to compare plan behavior before upgrading a workspace
• Use Billing and invoices if you need payment methods, invoices, or billing settings

New members joining an existing workspace

• Use the workspace dropdown to confirm you are in the right workspace before running a job
• Check Jobs to understand what history and results are visible in the active workspace
• Check Files and Collections to understand saved library files, uploads, and reusable collections

Run your first analysis

Once your workspace is ready, run a small analysis first so you can learn the submission and result flow.

Pick a first tool

Good first tools are fast, simple, and easy to verify:

• Protein Parameters: Calculate molecular weight, pI, and related sequence properties
• PDB to FASTA: Convert a structure file into one or more protein sequences
• ADMET-AI: Predict compound properties from SMILES input
• AutoDock Vina: Run a molecular docking workflow when you already have receptor and ligand inputs

Add input

Tool pages determine which input methods are available. Depending on the tool, you can paste text, upload files, or fetch records from external sources such as RCSB PDB, PubChem, or UniProt.

For a sequence tool, a FASTA input can look like this:

>Protein1
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK

Review settings and cost

Most tools can run with their default settings for a first pass. Before submitting, review the visible configuration, check the credit badge beside the submit button, and confirm your workspace has enough credits for the run.

If a tool shows 0 credits, the run is free. If a tool shows a paid cost, ProteinIQ deducts the credits when the job is created.

Submit the job

Click Submit job for server-side tools or Generate for browser-side tools. Server-side tools create a job with a tracked status, then update the result view when processing finishes.

The core job statuses are:

• Pending: The job was created and is waiting to start
• Processing: The job is actively running
• Completed: Results are available
• Failed: The job ended with an error
• Timeout: The job exceeded its execution limit

If a paid job fails or times out, ProteinIQ refunds the eligible credits automatically.

Review results and continue

Completed jobs show their outputs on the tool page. Depending on the tool, results can include tables, files, text output, plots, molecular structures, or downloadable artifacts.

Use these entry points after a run:

• History: Review jobs across the active workspace
• Files: Browse saved files, upload documents, and organize reusable outputs
• Usage: Check credits and recent usage
• Tool page history: Reopen previous runs for the current tool when the tool includes history

Ongoing resources

Use these docs as your next reference once you have run the first job.

• Concepts: Understand the core objects in ProteinIQ and how they fit together
• Jobs: Job statuses, history, retries, sharing, and downloads
• Credits: How charges, refunds, expiration, and balance tracking work
• Files and Collections: How saved files, uploads, and collections work
• Workspaces and seats: Workspace roles, shared usage, seats, and collaboration
• Pricing and billing: Plans, billing periods, credits, and subscription changes