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Changelog

Everything new on the ProteinIQ platform.

October 10, 2026

Eight new chemistry and sequence tools arrive, along with NuCaliby for designing coding DNA from protein backbones and task-based tool search

Workspace pages, job submission and tool search are faster, and many hosted tools now catch bad inputs before a run starts.

Added

  • Added Molecular similarity search, Chemical substructure search, Butina clustering, the Stereoisomer generator, Dimorphite-DL for ligand protonation and Codon optimization
  • Added SMILES to PDBQT and PDBQT to SDF converters for docking files
  • Added NuCaliby for designing coding DNA and protein sequences from backbones, with an interactive 3D viewer for backbone ensembles
  • Added task-based tool search, so searching "protein protein docking" or "folding" finds the right tools, plus a Task filter on the tools page
  • Added a downloadable approved drug library with 3D SDF files and docking benchmark datasets, with Load from dataset in molecule inputs
  • Added native SDF output to SMINA, mapped poses to AutoDock-GPU, downloadable design metrics to RFdiffusion3, and native modes, query lists and outputs to ScanNet
  • Added format conversion choices and keyed joins to the workflow editor
  • Added runnable examples to the docs, a Copy page menu, and a Markdown version of every public page at its .md URL
  • Added a Compact/Full toggle for wide result tables and next-step suggestions after downloading results

Improved

  • Improved speed when moving between workspace pages and tools, submitting jobs, searching the tool directory and following job progress
  • Improved scrolling in large molecular dynamics, GC content and open reading frame result tables
  • Improved input checks before submission in IQ-TREE, PRODIGY, ColabDock, AutoDock Vina, AIMNet2, RosettaFold3, RAxML-NG, Clustal Omega and DiffDock
  • Improved error messages in PDB2PQR, MolProbity, PDBFixer, Chai-1, ProteinMPNN and SDF to PDBQT
  • Improved the tool input panel with the job name and project in its header, a wider layout, compact setting tabs and settings shown directly for tools with few options
  • Improved pasted sequence handling, so wrapped sequences are read consistently and FASTA names are kept
  • Improved Caliby settings, model selection and BinaryCIF input, and raised the SMINA maximum runtime to two hours

Fixed

  • Fixed OpenFold 3 predictions with uploaded ligand structures, Genie 3 motif scaffolding on multichain structures and ScanNet submissions with PDB and UniProt identifiers
  • Fixed IQ-TREE rejecting CLUSTAL, PHYLIP and NEXUS alignments, FastTree ignoring zero support resamples, and PROPKA and PDB2PQR rejecting PDB files with charge columns
  • Fixed MOL and SDF files with blank molecule titles failing to convert, and hydrogens being dropped after pH correction in SDF to PDBQT
  • Fixed large electrostatic maps not loading in PDB2PQR results, viewer errors when measuring while removing structures, and file previews showing a previously opened file
  • Fixed chart export dialogs hidden in fullscreen, table statistics overlapping rows, and missing colors in workflow controls and charts
  • Fixed slow or failing workspace loads during busy periods, retrying a tool page after a loading error, and missing results for cancelled jobs fetched through MCP
October 4, 2026

SMINA adds flexible side-chain docking, and many hosted tools now expose more of their native settings and outputs

Many sequence calculators now handle FASTA descriptions, CSV and PDB inputs more reliably, and several of them return extra results.

Added

  • Added flexible side-chain docking, more scoring functions and more file formats to SMINA
  • Added a Guide tree tab to Clustal Omega and MAFFT results
  • Added custom checkpoint uploads to ProteinMPNN, custom dictionaries to DSSP, and a base checkpoint and ProtT5 embedding input to ABodyBuilder3
  • Added more settings and outputs to Boltz-2, Foldseek, US-align, ADMET-AI, AIMNet2, PoseBusters, PLIP, RFdiffusion, RAxML-NG, IQ-TREE, FastTree and PeptideBuilder
  • Added EUR pricing with a currency selector for customers in Europe

Improved

  • Improved paid plans by removing per-plan batch size limits
  • Improved the random DNA, random protein and random RNA generators with clearer settings and more reliable output
  • Improved input handling in the pI Calculator, Instability Index, glycosylation site finder, FASTA Splitter, FindPept and radius of gyration tools, with predicted stability, sequence contexts and mass match summaries in their results
  • Improved input checks for structured batch jobs and the messages shown for invalid ProLIF ligand files

Fixed

  • Fixed SMINA docking scores that were attached to the wrong pose
  • Fixed GROMACS final-frame selection, force-field setup and energy units, and AF-Cluster rejecting valid alignments and renaming sequences
  • Fixed results in amino acid composition, GRAVY, peptide mass, Peptide Cutter, the motif scanner and the CpG Island Finder when inputs had FASTA descriptions, unusual residues or overlapping matches
  • Fixed PDB to CIF conversion losing settings, occupancy values and extra models
  • Fixed phylogenetic trees missing branches, and the settings dialog closing when switching workspace
October 2, 2026

Eight new Boltz models and screening tools arrive, alongside DeepRank-Ab, DiffDock-PP and OpenDDE

Every hosted tool now runs on the Free plan, the workflow editor gains undo and pre-run checks, settings move into a searchable dialog, and workspace pages, viewers and tool pages load noticeably faster.

Added

  • Added Boltz-2.1, BoltzMol-1, BoltzProt-1, Boltz ADME, Boltz Protein Screen, Boltz Sequence Redesign, Boltz Small Molecule Screen and Boltz Small Molecule Explore
  • Added DeepRank-Ab for scoring antibody and nanobody complexes, DiffDock-PP for protein complex docking and OpenDDE for all-atom structure prediction
  • Added PRODIGY for binding affinity, StaB-ddG for mutation effects on binding and DeepRank-GNN-esm for interface scoring
  • Added BioEmu for sampling protein conformations, RAPiDock for protein-peptide docking, Caliby for sequence design and ProteusAI for prioritizing variants from measured fitness
  • Added ESMFold2 Binder Design, ESM-C Mutation Scoring and the overlapping peptide generator
  • Added AMBER19 and CHARMM36 force fields, more water and implicit-solvent models, missing-residue building and a crystal-water option to OpenMM
  • Added Meeko ligand settings and advanced receptor preparation to AutoDock Vina, template options and chain labels to Boltz-2, sequence receptors, PDB and PDBQT ligands and advanced sampling to DiffDock, and more settings to FreeBindCraft
  • Added undo, copy and paste, draft history and pre-run checks to the workflow editor, and workflow reruns now reuse jobs that already succeeded
  • Added a searchable settings dialog you can open from any page, with custom date ranges and a per-tool table for usage, and a data download in account settings
  • Added bulk team invitations with a role for each email
  • Added search and file type filters to job output files, Project and Status filters to Batches, and mmCIF input with residue and chain tables to the SASA calculator

Improved

  • Improved the Free plan so every hosted tool can be run on it, including OpenMM, OpenFE and binder design tools
  • Improved ProteinMPNN and LigandMPNN results with an interleaved alignment view and a Sequences tab for FASTA export
  • Improved the docking pose panel with a ligand filter and per-pose downloads, and made the MSA viewer smoother to scroll
  • Improved input checks before submission for PDBFixer, DSSP, GeoDock, ANARCII, ProLIF, DynamicBind, Chou-Fasman and MD trajectory analysis, and molecule inputs now accept 5-character CCD codes
  • Improved loading speed of 3D structure viewers, tool pages, workspace pages, workflows and the AI Assistant

Fixed

  • Fixed missing results from large Foldseek and RNAplfold runs
  • Fixed FlowDock jobs failing with multiple SMILES ligands and workflow steps rejecting proteins from earlier steps
  • Fixed SASA calculator results for selenomethionine and other modified residues, missing MD trajectory analysis charts, and aliphatic index results for FASTA descriptions and CSV and PDB uploads
  • Fixed run logs not opening for some failed jobs, panels blinking when opening saved results, and a crash when adding residue modifications
September 25, 2026

CatPred now predicts enzyme kinetics, and FreeBindCraft adds a second hosted option for binder design

FASTA conversion gets two new tools, and more docking and structure tools catch unusable inputs before a run starts.

Added

  • Added CatPred for predicting enzyme kcat, Km and Ki from sequences and SMILES, with uncertainty estimates for every prediction
  • Added FreeBindCraft for de novo binder design with default, beta-sheet and peptide protocols
  • Added the FASTA converter and FASTA to CSV converter
  • Added overall protein scores to Aggrescan3D results

Improved

  • Improved TXT to FASTA and GenBank to FASTA to recognize more sequence layouts in pasted text and documents
  • Improved DNA Shuffle with uniform shuffling and support for messy input, RNA and document uploads, and made seeded runs in the DNA mutation generator consistent
  • Improved fpocket so residue-defined pockets can be selected directly and structures with no detected pockets still return results
  • Improved AlphaFold2 support for very long inputs and kept the original error details when a prediction fails
  • Improved input checks before submission for Boltz-2 templates, PLIP, AutoDock Vina search boxes and multi-model receptors, AutoDock-GPU receptors, ViennaRNA, Aggrescan3D and PPAP
  • Improved speed of 3D pose viewing, batch validation and search, CSV previews and workflow runs
  • Improved input size messages on the free plan and made alignment format checks consistent across tools

Fixed

  • Fixed file previews losing their original formatting
  • Fixed workflow ligand inputs that rejected some supported file formats
September 18, 2026

Batches now accept CSV files that describe each job in full, and design and docking tools share a residue picker that works directly on the structure

Workflows also got a clearer vertical layout.

Added

  • Added CSV batches for named complexes, explicit file pairings and settings that vary between jobs
  • Added a shared residue picker to AutoDock Vina, ProteinMPNN, LigandMPNN, SolubleMPNN and Genie 3 for selecting residues on the structure preview
  • Added a way to report an input validation message you think is wrong directly from the input card
  • Added the option to hide the app sidebar, with a preview on hover

Improved

  • Improved workflows with a vertical layout, more reusable outputs, and clearer explanations when a credit estimate cannot be calculated
  • Improved AutoDock Vina to repair incomplete receptors automatically, including repaired structures passed in from workflows
  • Improved FlowDock with the shared structure viewer and faster input preparation
  • Improved input checks before submission for PepMimic, ProteinMPNN and PROPKA 3, and gave PROPKA more time for large structures
  • Improved Salmon to accept short reads

Fixed

  • Fixed 3D structure display for single molecules in SMILES to PDB and related SMILES converters
  • Fixed some valid structure and ligand files being rejected at upload
September 11, 2026

Batches can now pair inputs in order instead of running every combination, and ORF Finder and BioPhi results are easier to explore

Large tables, alignments and file libraries also load faster.

Added

  • Added a pairwise option to batches that matches inputs from separate lists in order instead of running all combinations
  • Added explorer, table and summary views to ORF Finder, with linked ORF selection and zoom
  • Added native geometry settings to PeptideBuilder and refinement controls to GeoDock

Improved

  • Improved BioPhi results with grouping by chain and sequence variant, and input checks before submission
  • Improved Admetica with grouped property selection
  • Improved speed of large result spreadsheets, the alignment viewer, large file libraries and 3D structure loading
  • Improved input checks before submission for DSSP, USAlign, Boltz-2 bonds and AutoDock Vina mmCIF ligands and flexible residues
  • Improved DSSP to explain empty result tables and PDB2PQR to show its run summary separately from pKa values

Fixed

  • Fixed batch downloads missing some result files
  • Fixed AutoDock Vina dropping some uploaded ligands
  • Fixed AlphaFlow showing selectors for inactive models
September 5, 2026

Ramachandran plot now makes individual residues easier to inspect, reports analysis coverage, and keeps filtered statistics and exports aligned with the plot

Added

  • Added a ready-to-run 1HNR example, direct PDB ID entry, keyboard and touch residue inspection, and an outliers-only filter to Ramachandran plot
  • Added per-residue skip reasons and separate current-selection and whole-structure CSV exports

Improved

  • Improved plot readability in narrow output panels with equal angle scales, separate residue-class reference views, degree labels, and numerical summaries

Fixed

  • Fixed angle calculation for incomplete neighboring residues, undefined geometry, and twisted-proline reference selection
August 24, 2026

AntiFold now returns per-residue embeddings, presents antibody design coordinates and sequence metrics more accurately, and reports invalid inputs and run failures more clearly

Added

  • Added optional source-native NumPy per-residue embeddings to AntiFold results and workflows, with lossless binary handoff between workflow steps

Improved

  • Improved AntiFold with chain-specific IMGT region choices, insertion-code-aware mutation coordinates, visible sequence loss and recovery metrics, and clearer raw perplexity guidance
  • Improved AntiFold run validation with reliable failure detection and actionable messages for malformed structures
August 21, 2026

A new DNA Ligation Calculator, a major Oligo Analyzer upgrade with Primer3 thermodynamic analysis, and more reliable large-input uploads across analysis tools

Added

  • Added the DNA Ligation Calculator for insert:vector molar ratios, required insert mass, fmol amounts, and reaction setup volumes

Improved

  • Improved Oligo Analyzer with Primer3 thermodynamic analysis; single-oligo, primer-pair, batch, and multiplex interaction modes; Mg²⁺ and dNTP reaction conditions; selectable Tm and salt-correction methods; named FASTA records; structured result tabs; and reusable workflow outputs
  • Improved upload reliability when submitting large inputs to analysis tools
  • Improved tool pages to display the exact deployed version for each analysis model
August 20, 2026

Product updates

Improved PDB2PQR with protein, DNA, RNA, PDB, and mmCIF support; pH-series comparisons; structured pKa and run-coverage tables; optional APBS electrostatic maps with interactive 3D viewing; complete native diagnostics; reproducibility manifests; and molecule-aware workflow outputs.

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