Peptides Release Notes

This page lists what shipped in each early-access release of the Peptide feature, newest first. Every entry describes a change you can see in the application; internal refactors are mentioned only where they change behaviour.

v3.0.0-early-access-2026-09-22

Fourth early-access release: side chemical chains on the canvas, a reorganized viewer toolbar, structures readable at high zoom, a Sync monomers action for whole datasets, and import issues that say whether a structure is in the dataset.

New

Peptide viewer

• Side chemical chains. A chemical object can carry further chemical objects (a PEG spacer ending in a biotin, for example). The viewer now draws the whole chain, one node per object. Chains of several objects open grouped as one pill (3 chems); hover it and click +, or right-click and choose Ungroup Chem Chain, to see the objects. See How to Explore the Peptide Viewer.
• Galleries compare whole chains. A chemistry gallery shows one column per distinct chain, named with a short notation such as K - PEG2 >R² Biotin. Filters, hotspots and synergies use the same whole-chain identity.
• Chemical chains on a branch residue (a GLP-1 lipidation on its γGlu spacer, for example) are now drawn, shown and hidden with their branch. Gallery, side-chain filter, hotspot impact and alignment editor mark them on the branch residue.
• Toolbar menus. The More and Reset Layout buttons are replaced by five menus: Layout, Monomers, Regions, Bridges and Chem chains. They add Select All Monomers, Collapse / Expand All Regions, Expand / Collapse All Linkers, Group / Ungroup All Chains and Expand / Collapse All Chems. The canvas right-click menu offers the same groups, plus the selection actions while something is selected.
• Reset Position on monomers, chemical objects and bridge linkers, and Reset Layout of Selection on the selection toolbar.
• Chemical objects and bridge linkers can be selected, expanded and collapsed like monomers. A bridge linker can be resized, and its expanded structure keeps the proportions of the molecule.
• Zoom in to see the structures. Zoomed in, every monomer and chemical object shows its structure inside its bead. Toggle with Show Structures at High Zoom in Settings → Display.
• Expanded monomer size slider in Settings → Display, resizing all expanded monomers at once.
• Smart Guides. Dragged monomers, regions and galleries snap to the surrounding rows, columns and edges. On by default; toggle it in the Layout menu.

Datasets

• Sync monomers for a whole dataset, from the dataset title bar. Use it after a monomer was corrected in the Biotoolkit Monomer Service. See How to Resolve Missing Monomers.
• Export the import issues as CSV (structure-issues.csv): source, identifier, outcome, missing data, structure and error of each entry.
• Canonical SMILES and InChIKey columns for peptides, with Copy actions in the row menu. Run Sync monomers to fill them on older datasets.
• The monomer library picker explains when a file is needed and where monomers live.

Improved

• Chemical objects follow their attachment point. In linear layouts, a chemical object bonded on R1 sits before its residue or parent object, on R2 after it, on any other R-group above it. Cyclic layouts stay radial.
• Import issues are grouped into Peptides not imported, Peptides imported with missing data (naming what is missing) and Monomers not registered (now including rows the Monomer Service refused, with its reason). See How to Resolve Missing Monomers.
• Macrocycles open in cyclic layout. The Linear / Cyclic toggle is shown only for macrocyclic peptides; your saved layout or your own switch is always kept.
• Only the three strongest synergies are drawn as regions by default; tick more in the synergy list. See How to Analyze Hotspots and Synergies.
• Clear position filters appears only while a filter is active, and covers side-chain and bridge filters too.
• Keep Only Selection Variable also locks the reference's side chemical chains.
• Expanded chemical objects are drawn inside a thin coloured ring instead of a filled box.
• Deleting an alignment from the alignment list now asks for confirmation.
• Monomer library files are read more leniently: header names are matched loosely, R1, R2… columns are accepted, and an unreadable row is skipped and reported instead of failing the file. See How to Create a Peptide Dataset.

Fixed

• Molecular weight and atom count were wrong on HELM datasets because free attachment points were capped with hydrogen instead of the declared cap group. Run Sync monomers on older datasets.
• Peptides whose structure converted only partially — a monomer left out of the computed properties, molecular properties that could not be computed, an internal conversion error — were stored without being reported. They are now listed under Peptides imported with missing data.
• An outage of the HELM validation service no longer reports every HELM peptide as invalid: the peptides are converted anyway.
• Peptide slides ignored the sort criterion shown in the sort panel.
• Mouse wheel and trackpad did not zoom over galleries, monomers, regions or cyclization hubs.
• Right-clicking a second node only closed the first node's menu.
• A right-click or a tiny mouse move was taken as a drag and made expanded structures jitter.
• On a macrocycle, a region spanning the ring closure could not be collapsed.
• A collapsed region inside a cyclization was drawn after the ring, on the backbone, while the ring kept empty places for the hidden residues. It now takes one place on the ring. A collapsed region hiding a bridge end lays the cycle flat on the backbone instead.
• Branch and user regions sometimes swapped fill colours.
• After dragging a residue, the marker and gallery of a non-reference chemical object stayed at the old position.
• Expand / Collapse Selected ignored chemical objects and bridge linkers.
• Create Region and Cyclize Selection counted linkers and regions as residues.
• Deleting a default-visible synergy region did nothing.
• Attachment-point atoms in expanded structures were drawn black; they now keep their element colour.
• Peptides with inlined + monomers reported a spurious conversion warning and a wrong monomer count.

v3.0.0-early-access-2026-08-18

Third early-access release. It is a feedback release, focused on the issues you reported: branches, alignment editing, monomer libraries, and viewer rendering.

New

• Reassign a peptide's side chain to another branch. In the alignment editor, right-click a backbone cell carrying a branch to move it to another branch or split it off into its own. See How to Align Peptides.
• Text endpoints are now supported. A string property used to show a dash or an empty cell; it now displays everywhere peptide values are shown, with its own aggregation options (most frequent value by default, or a per-category bar chart for properties with few values). Numeric analyses (hotspot, synergies and charts) simply skip text endpoints. See How to Explore the Peptide Viewer.
• Monomers registered from Ideation survive a Biotoolkit Monomer Service outage. Ideation keeps a copy of each registration and falls back to it when the service is down, so your datasets still open and render. The service stays the source of truth and always wins when reachable. See How to Resolve Missing Monomers.
• Filter by Peptide ID in the viewer. The Filters panel now has a Peptide ID column, so you can narrow the canvas to named peptides directly.
• Edit the alignment from the peptide list. An Edit Alignment button opens the editor on the alignment in view; Save as new switches the viewer to the new alignment.
• Bridges through a chemical linker are now drawn as bridges. They used to be dropped by the viewer. The linker is drawn as a node in the middle of the bridge — expand it to see its structure, or drag it to reshape the arc. All bridges between the same two residues are shown as one bridge, with each linker, the direct bridge and the unbridged peptides as gallery variants, and the linker's name shown in tooltips, cards and badges. See How to Explore the Peptide Viewer.
• Bridges, chemical objects and branch attachments are shown in the alignment editor, with the same indicators as the viewer's peptide list, and they follow your gap edits live.

Improved

• The monomer library file now uses the Biotoolkit Monomer Service's field names, so one file imports into both applications. Only the symbol and a structure (smiles or ctab) are required, unknown columns are ignored, and the downloadable templates were updated to match. Files in the previous Ideation format still import unchanged. See How to Create a Peptide Dataset.
• Your library file is now authoritative. Polymer type, monomer type and R-group cap groups declared in the file are used as-is instead of being replaced by guessed values.
• More SMILES attachment-point notations are accepted. N[R1], N[1*] and N[H:1] now register identically to N[*:1]. An attachment point with no R-number is reported as an error naming the monomer. This applies to monomer libraries uploaded through Ideation only, not to monomers registered directly in the Biotoolkit Monomer Service.
• Bridges are much easier to hit. Pointing anywhere near a bridge now picks the nearest one — no more pixel-perfect aiming for the tooltip or right-click menu.
• The dataset page's structure column is named "Backbone Sequence" on a peptide dataset; small-molecule datasets keep "Structure".
• Hotspot scores now match what each element's gallery shows. A residue is scored by its monomer substitutions, a chemical object by the chemistry at its attachment (shown on the chemical node itself), and a bridge by its own variants — fixing scores that were previously shifted to the wrong residue or unrelated to the gallery. See Understanding Hotspots and Synergies.
• The hotspot endpoint list matches the slide. It now lists only the numeric endpoints on display, under the labels you configured, and defaults to the slide's main endpoint.

Fixed

• Editing the alignment could split one side chain into two half-empty branch tabs. Branch identity no longer depends on alignment edits, and branches are numbered consistently everywhere.
• A side chain bonded through its C-terminus was drawn crossing back over its own backbone residue. The connector now lands on the residue that actually carries the bond, and C-terminal branches extend leftwards.
• Dragging a monomer out of a collapsed branch sent it to the top-left corner of the canvas, and a moved branch crept leftwards on every redraw.
• Switching chains in the alignment editor could leave position columns blank; the same problem in the peptide list table is fixed too.
• An expanded monomer's free attachment points were capped with a plain hydrogen — a C-terminal residue was drawn as an aldehyde instead of a carboxylic acid. Free attachment points now use the cap groups the Biotoolkit Monomer Service declares. See How to Explore the Peptide Viewer.
• Inside a branch tab, the residue that bonds to the backbone is now marked in the cell corner and explained in the tooltip.
• The corner badges on peptide-table cells swallowed the pointer, blocking hovers and clicks.
• Releasing Ctrl mid-drag froze a rectangle selection on the canvas.
• The final step of the Create Dataset dialog could not be scrolled.
• The alignment step of the create-slide drawer showed the word "Alignment" twice.
• Monomers per Line broke the row too early when a cyclization held an expanded monomer; the row now simply grows wider.
• Collapsing a branch made the hub of a region reaching into it jump away; it now stays where you left it.

v3.0.0-early-access-2026-08-07

Second early-access release. The theme is alignment: you no longer have to bring your own.

New

• Every peptide dataset now arrives aligned. Import runs a Generating Alignment step and stores the result as an alignment named Default alignment with an AUTO badge, so you can create a SAR Slide without providing any file. The step is best-effort — it is skipped when no peptide carries a HELM sequence, or when the dataset holds more than 5,000 peptides — and a skipped alignment never fails the import. See How to Align Peptides.
• Generate an alignment on demand. New Alignment › Generate automatically aligns the dataset's own sequences at any time. It always adds an alignment and never overwrites an existing one, so a computed frame can be compared side by side with a curated one.
• Gap costs adapt to the dataset. Gaps are charged heavily across uniform-length peptides, so none are invented, and lightly across series carrying real insertions or terminal extensions, so those stay gapped. See Understanding Peptide Alignment.
• Alignment import no longer aborts on mismatches. Peptides that match the dataset are imported, and every issue — a missing or unknown identifier, a sequence that differs from the dataset, an ignored sheet, a non-common backbone — is reported as a warning on the alignment instead of failing the whole file. Import fails only when the file is unusable or nothing matches, and those cases now return a clear message rather than a generic error.
• Repair warnings in the alignment editor. Warnings raised by an import are listed per alignment and can be resolved directly in the editor, so a nearly-correct file no longer has to be fixed outside Ideation and re-uploaded.

Improved

• Multi-sheet Excel alignments. For datasets with branches, import walks two steps before saving: pick the sheet holding the backbone (or declare there is none), then map the remaining sheets to the dataset's branches. Without a backbone sheet the frame is rebuilt from the dataset's HELM and any unmapped branch is left-aligned.
• Monomer sync lives in the skipped-structures dialog. The missing-monomer list, the link to the Biotoolkit Monomer Service and the sync action are now in one place, reachable everywhere that dialog appears — dataset view, settings drawer, import timeline and item lists. The standalone sync button is gone.
• Peptides now run in their own service. Peptide imports, conversions and alignments are processed by a dedicated peptide service with its own queue, so they no longer queue behind small-molecule jobs.
• Cap groups are read from the monomer structure when you upload a monomer library, instead of being guessed from the symbol — fewer monomers need manual correction after import.
• Synergy exploration reworked. The Explore Combinations table was rebuilt, the threshold slider and region controls were reworked, and synergies involving positions hidden by your gap display options are no longer offered — a set you cannot see on the canvas is no longer proposed.

Fixed

• Clustering could produce wrong groups because of a bug in the clustering worker.
• Hotspot badges were drawn in the wrong place on bridges.
• The Hot / Warm / Cold ranges in the hotspot legend and its help tooltip were fixed to the default cut-offs, so they were wrong as soon as you moved the thresholds. They now follow the values you configured, and dragging the threshold slider recomputes the analysis once on release instead of on every tick.
• The Biotoolkit Monomer Service link in the missing-monomer dialog did not always point at your organization's instance. It is now resolved when you open the dialog, from the address you are working on.
• The Clusters tab in the SAR Report settings drawer clustered differently from the docked Clusters panel: it fell back to the standard-residue table, so every non-natural monomer scored a full mismatch. Both now use the dataset's monomer definitions.
• Peptides whose structure had not been fully converted were not always detected, so they were skipped without being reported.
• The downloadable peptide dataset CSV template had a mismatched number of columns.

v3.0.0-early-access-2026-07-07

First early-access release of the Peptide feature.

Peptide datasets

• New Peptide dataset type, imported from CSV or Excel with a HELM column, or from an SDF. Semicolon-delimited (French) CSVs are supported.
• Upload a monomer library with the dataset (CSV, Excel or SDF) to describe non-natural monomers. Monomers embedded in a V3000 SDF are extracted and registered automatically.
• An import status timeline with the peptide-specific steps, and a skipped structures dialog listing the peptides that could not be converted.
• Peptides whose monomers are unknown to the Biotoolkit Monomer Service are reported as missing monomers, with a link to register them and a sync action that re-runs conversion once they exist. See How to Resolve Missing Monomers.
• A dataset-level default reference peptide, preselected when you create a report.

Peptide SAR Reports

• Peptide is a first-class SAR Slide type in the Create SAR Report dialog, alongside MMP and RGD, shown when the peptide plugin is licensed.
• Import an alignment from CSV or Excel, review it in the alignment editor, and choose which position numbering starts from (Set as first position).
• Alignments belong to the dataset, so several slides in one report can use different alignments over the same peptides.

The peptide viewer

• An interactive canvas showing the backbone, branches, chemical objects and bridges of the reference peptide, with a per-position gallery of the variants observed across the series and their endpoint values.
• A peptide list drawer with the full table of peptides and their properties.
• Filtering down to the peptides that differ from the reference at chosen positions.
• Custom canvas layouts, saved and restored per slide, with reset actions grouped in their own menu.
• Image download of the canvas.

Analyses

• Hotspots — per-position impact with Hot / Warm / Cold badges, thresholds you control, and a baseline chosen between average, median and the reference peptide's value. See Understanding Hotspots and Synergies.
• Synergies — pairs and triples of positions that depart from an additive model, with interaction strength, direction, an explore-combinations table, and region support.
• Clustering — grouping of the series with a cluster explorer, quality figures and a scatter view; branches and specific chemistries are taken into account. See Understanding Peptide Clustering.

Endpoints and display

• A per-endpoint aggregation type and a dedicated Endpoints tab in the peptide SAR Report settings.
• Number formatting, value coloring and sort direction from the endpoint settings applied everywhere peptide values are shown — galleries, enlarged galleries and the peptide table.
• Molecule rendering settings applied to every peptide structure render, including expanded monomers and gallery tooltips.

Version reference