Changelog

January 23, 2026

Major release introducing AI-powered antibody design tools, ADMET prediction, and an AI assistant for bioinformatics guidance.

Improvements (6)

• Added IgGM generative foundation model for antibody and nanobody design with CDR design, affinity maturation, and structure prediction capabilities.
• Added IgDesign antibody CDR sequence design via inverse folding for therapeutic antibody development.
• Added AntiFold inverse folding tool for antibody variable domain structures using IMGT numbering.
• Added Admetica ADMET property prediction using Chemprop-based machine learning models for 22 pharmacokinetic and toxicity endpoints.
• Added gmx_MMPBSA binding free energy calculator using MM/PBSA and MM/GBSA methods for protein-ligand, protein-protein, and protein-DNA complexes.
• Added AI Assistant chat interface for getting bioinformatics guidance, tool recommendations, and help interpreting results.

Fixes (1)

• Fixed ProstT5 tool that was failing to process sequences correctly.

January 15, 2026

New tools for molecular dynamics analysis and enzyme kinetics prediction.

Improvements (2)

• Added MD Trajectory Analysis tool using MDAnalysis to calculate RMSD, RMSF, radius of gyration, hydrogen bonds, PCA, and 20+ other analyses from MD simulation trajectories.
• Added DLKcat deep learning model for predicting enzyme turnover numbers (kcat values) from protein sequences and substrate structures.

January 11, 2026

This release expands the platform with new AI-powered protein design tools, antibody language models, and drug discovery compound screening filters.

Improvements (11)

• Added ODesign all-atom generative AI for designing protein binders with precise control over target binding sites and interaction parameters.
• Added MiniFold ultra-fast single-sequence protein structure prediction, 10-20x faster than ESMFold with no MSA required.
• Added EvoPro genetic algorithm-based protein binder optimization using AlphaFold2 fitness evaluation and ProteinMPNN sequence design.
• Added CleaveNet AI-powered prediction of matrix metalloproteinase (MMP) cleavage sites for peptide sequences.
• Added AbLang antibody residue restoration using a language model trained on the Observed Antibody Space database.
• Added AbLang-2 antibody-specific language model for predicting non-germline residues with germline bias correction.
• Added PAINS Filter to screen compounds for pan-assay interference patterns that cause false positives in biological assays.
• Added Brenk Filter to identify toxic, reactive, and pharmacokinetically problematic molecular fragments.
• Added Veber's Rule calculator to predict oral bioavailability by evaluating molecular descriptors.
• Added Lead-likeness Filter for stricter compound screening in early-stage drug discovery.
• Added new Security page at /security outlining platform security practices.

January 6, 2026

New tool for identifying ligand binding pockets in protein structures, plus critical validation improvements for Boltz-2 and PDB2PQR.

Improvements (1)

• Added fpocket protein pocket detection tool using Voronoi tessellation to identify binding sites with druggability scores, volume, and polarity analysis.

Fixes (2)

• Added Boltz-2 guardrails for protein structures that exceed 1,400 residues.
• Fixed PDB2PQR accepting small molecule PDB files and failing with unclear errors.

January 3, 2026

Expanded the platform with new AI-powered tools for protein stability and molecular property prediction.

Improvements (3)

• Added PepMLM peptide masked language model for generating sequence embeddings and predicting peptide properties.
• Added SmrTNet deep learning model for predicting small molecule retention times in liquid chromatography.
• Added ThermoMPNN protein thermostability prediction tool using message passing neural networks to estimate melting temperatures.

Fixes (1)

• Fixed MolProbity and PDB2PQR failing on PDB files starting with CRYST1 records instead of HEADER/ATOM.

January 2, 2026

New tools for antibody analysis and nanobody binder design join the platform.

Improvements (2)

• Added IgBLAST immunoglobulin and T cell receptor sequence analysis tool for identifying V/D/J gene segments and CDR regions.
• Added mBER VHH nanobody binder design tool using AlphaFold-Multimer to generate novel antibody sequences.

December 31, 2025

New tools for docking quality assessment, conformational ensemble generation, and toxicity prediction join the platform.

Improvements (5)

• Added DockQ docking quality assessment tool for comparing predicted structures against native references with DockQ scores, iRMSD, LRMSD, and fnat metrics.
• Added AlphaFlow protein conformational ensemble generator using flow matching to explore protein flexibility and dynamics.
• Added eToxPred machine learning-based toxicity and synthetic accessibility prediction for drug candidate screening.
• Added AutoDock-GPU GPU-accelerated molecular docking using the AutoDock4 force field, up to 56x faster than CPU docking.
• New General Settings page at Settings → General for managing profile information, work type, active sessions, and account settings.

December 23, 2025

Enhanced chart-based analysis tools with better data access and export options.

Improvements (2)

• Enhanced Hydrophobicity Plot and Hydropathy Plot with tabbed Chart/Data views and improved export options.
• Improved API performance with signed URL caching for faster file downloads.

Fixes (2)

• Fixed RFdiffusion3 failing on PDB structures with missing residues (gaps in numbering).
• Fixed AlphaFold2 failing due to model weights not loading correctly.

December 14, 2025

• Added IQ-TREE phylogenetic tree builder with maximum likelihood and automatic model selection (ModelFinder).
• Added MUSCLE5 multiple sequence alignment using the PPP algorithm for high-quality alignments.
• Added HMMER for sensitive homology search using profile hidden Markov models to detect remote homologs.
• Added HADDOCK3 integrative protein-protein docking platform guided by experimental data.
• Added MSA Viewer interactive visualization for multiple sequence alignments with color schemes.
• Added ProstT5 protein language model for bidirectional translation between sequences and 3Di structural tokens.
• Added full-screen mode for tool outputs with expanded visualization controls.
• Added batch submission functionality for submitting multiple jobs at once with progress tracking.

December 13, 2025

• Added DSSP secondary structure assignment tool using hydrogen bond-based analysis (gold standard method).
• Added SASA Calculator for calculating solvent accessible surface area using the Shrake-Rupley algorithm.
• Added RMSD Calculator to compare protein structures with automatic Kabsch alignment.
• Added GenMol NVIDIA generative AI model for creating novel drug-like molecules using masked discrete diffusion.
• Added DynamicBind AI-powered protein-ligand binding prediction with conformational change modeling.
• Added BindCraft de novo protein binder design using AlphaFold2 backpropagation and ProteinMPNN.

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

• Added Ramachandran Plot visualization tool for analyzing protein backbone dihedral angles.
• Added six new protein property calculators: Aliphatic Index, Extinction Coefficient, GRAVY, Instability Index, isoelectric point, and Molecular Weight.
• Added job sharing functionality - share your analysis results with collaborators via shareable links.

November 25, 2025

• Added DNA to RNA and RNA to DNA sequence conversion tools.
• Added CIF format support for BoltzGen structure inputs.

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

• Added three new tools from the same model family: LigandMPNN, ProteinMPNN, and SolubleMPNN.

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

• Added DiffDock-L AI-based molecular docking model.
• Added the Guides section.

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

• The first set of cloud compute tools now generally available, including protein parameters calculator, ADMET-AI, and others. Browse all tools.
• Added FASTA splitter utility tool.

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.