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Changelog

Everything new on the ProteinIQ platform.

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September

September 5

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

August 24

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

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

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.

August 19

Product updates

Improved PROPKA 3 with pH, folding-profile window, and stability-grid controls, broader chain and residue selectors, partial-batch results, native warnings, and curated run logs.

August 14

New Logs panel

New feature: View run details for selected tools, starting with AutoDock Vina, Boltz-2, and TXT to FASTA.

New features: Workspace members and seats can now be viewed and managed in one place, and DeepImmuno now supports peptide generation and HLA scanning.

Fixes and improvements: Job results stay visible during refreshes, workflow results are easier to inspect, and result tables handle larger outputs better.

Fixes and improvements: Reverse Complement now handles FASTA and FASTQ records, RNA sequences, record names, and downloads more reliably.

August 7

Tool and workflow updates

New features: Metered tools and workflows now support credit budgets and warn when a run is close to using its budget.

New features: PocketXMol now supports peptide docking, AIMNet2 supports batch prediction and structure optimization, and OpenMM runs can continue from Amber restart files.

Fixes and improvements: Tool results remain available when navigating through browser history, and workflow files are preserved when switching inputs.

Fixes and improvements: Structure viewing, molecule parsing, input validation, and result downloads are more reliable across tools.

July

July 30

Product updates

Improved AF-Cluster with native alignment validation, accurate clustering settings and documentation, submitted-MSA provenance, captured diagnostic logs, and reusable A3M, TSV, PCA, and log workflow outputs.

Improved AF2BIND with verified source execution and model assets, calibrated score guidance, selected-chain validation, multi-model PDB support, interactive structure viewing, amino-acid activation heatmaps, native logs, and reusable CSV workflow output.

July 29

Product updates

Improved MiniFold with verified MiniFold execution and model assets, strict single-sequence validation, accurate mean pLDDT reporting, complete provenance, and native diagnostic logs.

July 28

Product updates

Improved ABodyBuilder3 with source-supported unknown residues, unambiguous paired-chain input, verified published model assets, reproducible runtime dependencies, complete provenance, and reusable PDB and pLDDT workflow outputs.

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