Quickstart

Get up and running with ProteinIQ in minutes. This guide covers the essentials.

1. Visit proteiniq.io and sign in
2. Choose a tool from the dashboard
3. Add your data via text, file upload, or database ID
4. Run the tool and download results

Choose a tool

Browse tools by category or search for specific functionality. Each tool shows its input requirements and what it produces.

Start with these:

• PDB to FASTA - Extract protein sequences from structure files
• Protein Parameters - Calculate molecular weight, pI, and extinction coefficient
• AutoDock Vina - Dock small molecules to protein targets
• ADMET-AI - Predict drug-like properties from SMILES

Explore all tools →

Add your data

ProteinIQ accepts data in three ways depending on the tool:

Text input

Paste sequences, SMILES strings, or structure data directly:

>Protein1
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK

File upload

Upload common bioinformatics formats:

• Protein structures: .pdb, .cif, .mol2
• Sequences: .fasta, .fastq, .gb
• Small molecules: .sdf, .mol, .smiles

Database IDs

Fetch structures and molecules directly from public databases:

• RCSB PDB: Enter PDB ID (e.g., 1ABC)
• PubChem: Enter compound ID or name

Configure settings

Most tools work with default settings. Expand "Advanced settings" to customize:

• Molecular docking: Number of poses, search space, energy cutoffs
• Protein design: Sampling temperature, number of sequences
• Analysis tools: Calculation methods, output formats

Run and download

1. Click "Run" to start processing
2. Wait for results - simple tools finish instantly, ML models take 1-5 minutes
3. View results in the browser
4. Download as CSV, PDB, or raw output files

Common workflows

Convert file formats

Need a sequence from a structure file?

1. Go to PDB to FASTA
2. Upload your .pdb file or enter a PDB ID
3. Download the FASTA sequence

Calculate protein properties

Preparing a manuscript table?

1. Go to Protein Parameters
2. Paste your protein sequence
3. Get molecular weight, pI, extinction coefficient, and more

Predict drug properties

Screening compounds before synthesis?

1. Go to ADMET-AI
2. Paste SMILES strings (one per line)
3. Get absorption, distribution, metabolism predictions

Molecular docking

Finding binding poses?

1. Go to AutoDock Vina
2. Add protein structure (PDB file or ID)
3. Add ligand (SMILES or SDF file)
4. Configure binding site
5. Run docking and visualize poses

View detailed docking tutorial →

Data privacy

• Client-side processing: Simple tools run in your browser
• Server processing: ML models run on secure infrastructure
• Private by default: Your research data is never sold or shared
• Secure storage: Data stored only for job history and results retrieval

Usage limits

Free tier includes:

• Unlimited format conversions
• Unlimited basic analysis tools
• Limited ML-powered predictions

View pricing for unlimited access →

Need help?

Tool not working?

• Check input format requirements
• Verify file size limits
• Try with example data first

Questions about a specific tool?

• Read the tool documentation (click "?" icon)
• Check parameter descriptions
• View example inputs/outputs

Technical support

• Email: support@proteiniq.io
• Documentation: proteiniq.io/docs

Next steps

• Browse all tools to see what's available
• Read the glossary for terminology and concepts
• Join the community to share workflows

Ready to start? Launch ProteinIQ →