ProteinIQ
Changelog

Changelog

December 12, 2025

  • Added Smart Actions dropdown to tool outputs for quick access to common actions like sending results to another tool.
  • Added ESM-2 protein language model for generating sequence embeddings useful for machine learning pipelines.
  • Added ESM-IF1 inverse folding tool to design protein sequences from 3D backbone structures.

December 10, 2025

  • Added RFdiffusion3 all-atom generative diffusion model for designing protein binders, enzymes, and symmetric assemblies.
  • Added RosettaFold3 open-source structure prediction for proteins, nucleic acids, and small molecule ligands.
  • Added Hydrophobicity Plot visualization tool for analyzing protein hydrophobicity profiles using multiple scales.
  • Added MolProbity structure validation tool with clashscore, Ramachandran, and rotamer analysis.
  • Added PROPKA 3 for predicting pKa values of ionizable residues in protein structures.

December 8, 2025

  • Added AlphaFold2 structure prediction via ColabFold with MSA-based folding for proteins and complexes.
  • Added MAFFT multiple sequence alignment tool for accurate alignment of protein and nucleotide sequences.
  • Added FoldSeek structure search tool for finding structurally similar proteins in databases.
  • Added Radius of Gyration calculator for measuring protein compactness from PDB structures.

December 6, 2025

  • Added Clustal Omega multiple sequence alignment tool for large-scale protein sequence alignments.
  • Added FastTree phylogenetic tree builder for rapid construction of evolutionary trees from alignments.
  • Added MMseqs2 ultra-fast sequence searching and clustering tool.
  • Added USalign structure alignment tool for comparing and superimposing protein structures.
  • Added ParaSurf binding surface prediction tool for identifying protein-protein interaction sites.
  • Added PDB2PQR for preparing structures for electrostatics calculations with PROPKA integration.

December 5, 2025

  • Added Protenix open-source AlphaFold 3 implementation for predicting protein, RNA, DNA, and ligand complexes.
  • Added CSV to FASTA converter for transforming tabular sequence data into FASTA format.

December 4, 2025

  • Added ESMFold protein structure prediction using Meta's evolutionary scale modeling.
  • Added OpenFold 3 open-source structure prediction model.
  • Added PocketFlow binding pocket detection and analysis tool.

December 3, 2025

  • Added Hydropathy Plot visualization tool for analyzing protein hydrophobicity profiles.
  • New dashboard recent jobs and quick actions.
  • Added SVG export functionality for chart visualizations.

December 1, 2025

  • Added SMINA molecular docking tool with improved scoring functions for virtual screening.
  • Added ColabDock protein-protein docking tool with distance restraint support for guided docking predictions.

November 29, 2025

  • Added Chai-1 state-of-the-art biomolecular structure prediction model supporting proteins, nucleic acids, and small molecules.
  • Added RFDiffusion 2 next-generation protein backbone design with improved unconditional generation.

November 27, 2025

November 25, 2025

November 24, 2025

  • Added Boltz-2 biomolecular foundation model for structure and binding affinity prediction. It's currently in early beta.
  • We made four of our premium tools now free: Protein parameters, Amino acid composition, Chou-Fasman, and protein stability. Guests can submit up to 10 FASTA sequences at a time, while logged in users (even on the Free account) can submit unlimited number of sequences. Previously, these tools cost 1 credit per FASTA.

November 23, 2025

  • Added LightDock protein-protein docking tool using Glowworm Swarm Optimization for predicting macromolecular binding modes.

November 22, 2025

  • Added citation functionality - tools now include citation snippets for academic use.
  • Added documentation for Text to FASTA converter with usage examples.
  • Enhanced molecular docking visualization with improved 3D rendering controls.

November 21, 2025

  • ProteinIQ now automatically generates citations for the tools you use. You can find them button in the bottom right part of the header. We'll be adding support for this feature to all the tools soon.

November 19, 2025

  • Added RFDiffusion protein structure design tool for generating novel protein backbones with diffusion-based modeling.
  • Enhanced legal documentation: added Computational Usage Policy, Content Policy, DMCA, and Data Processing Agreement.
  • Improved DNA to Protein translator with better validation and documentation.

November 16, 2025

  • Enhanced documentation section with new guides on Credits, Jobs, Pricing, and Quickstart.
  • Improved credit calculation system with tool-specific calculators including atom-count-based pricing for BoltzGen.

November 14, 2025

  • New Usage Dashboard at Settings → Usage showing credit consumption history, job statistics, and usage analytics with interactive charts.
  • New Billing Management at Settings → Billing for managing subscriptions, viewing invoices, and updating payment methods.

November 12, 2025

  • Stripe integration improvements for smoother checkout, subscription management, and payment processing.
  • Fixed SMILES validation to properly handle edge cases.

November 11, 2025

  • Added one of the best models of 2025: BoltzGen. BoltzGen is an expensive model to run and thus requires at least 200 credits, depending on the parameters chosen.

November 8, 2025

November 5, 2025

  • Added GNINA molecular docking tool with advanced CNN-based scoring and energy minimization.
  • Improved 3D molecular docking visualization with enhanced ligand-protein rendering and interactive controls.
  • Enhanced job polling system for more reliable real-time result updates.

November 3, 2025

  • Added Autodock Vina molecular docking tool with flexible ligand-protein binding predictions.

November 1, 2025

October 23, 2025

  • Major improvements to how you input sequences and files into tools, both free and paid tools.

October 22, 2025

  • Rebuilt the Protein stability prediction tool from the ground up. It's now more solidly based on peer-reviewed methods.
  • Added real-time input validation for SMILES, FASTA, AND PDB inputs, catching invalid formats before job submission. This means 90% fewer job errors.

October 19, 2025

  • Added the FASTA to FASTQ converter which assigns mock quality scores to FASTA sequences.

October 18, 2025

  • All tools now share the same improved interface with horizontal input and settings on the left and output on the right. You can simply wait for the results of your job on the same page or you can come back later at any time and access your past jobs via the "History" in the output panel. All tools share the same layout, which makes it easier for you to pick and start using new tools immediately.
  • Improved and added new settings to the One to three converter.

October 13, 2025

  • PDB Fixer now supports solvent box and lipid membrane addition for molecular dynamics simulations, with configurable ion types and box geometries. Performance improved from several minutes to ~40 seconds. We also updated the pricing for PDB Fixer, reduced from 5 credits flat to 2 credits base + multiplier based on atom count.

October 8, 2025

  • ProteinIQ now has a dark mode. You can switch between Light, Dark, and System modes by clicking your user icon in the bottom left or through the footer.
  • DNA mutator has improved color coding and now works as expected.

October 7, 2025

August 30, 2025

  • More tools, including server-side compute now available.

May 25, 2025

  • ProteinIQ launches with 13 browser-based molecular analysis tools covering protein parameters, drug discovery (Lipinski, toxicity prediction), sequence processing (FASTA/FASTQ conversion, translation), and structure visualization.
  • No installations or expensive licenses required—cloud infrastructure scales automatically with batch processing support and standard format exports.
  • Roadmap includes AlphaFold integration, molecular dynamics, protein design tools, and API access for pipeline integration.