Prerequisite: Load The Molecule From ChemrytIQ

Before opening ChemrytIQ-QSAR, search the molecule in ChemrytIQ by SMILES, InChI, molecule name, or CAS number. Confirm the correct molecule on the ChemrytIQ page, then open the required Chemryt app from that same molecule context so the selected structure is loaded into the app automatically.

What It Does

ChemrytIQ-QSAR submits molecule SMILES and selected endpoints to server-side prediction APIs, runs model inference, and returns endpoint-level ADME, toxicity, physicochemical, environmental, and safety signals with interpretation context.

Endpoint lanes

Fast QSAR, Fast Lane, Slow Endpoints, and EHS Endpoints run different endpoint scopes from the QSAR model library.

Model representation

Select SMILES, SELFIES, or both to control which model representation endpoints are submitted and how results are separated.

Result tabs

Read the combined QSAR tab first, then compare SMILES Endpoints and SELFIES Endpoints tabs when both representations are available.

Quick Tutorial

Load a valid molecule in ChemrytIQ and confirm the canonical SMILES before opening QSAR.
In Model, select SMILES for the standard chemistry string model, SELFIES for the robust SELFIES representation, or both when you want side-by-side representation evidence.
Run Fast QSAR first. It runs the priority 12-endpoint panel and quickly populates the Latest QSAR Run summary plus the QSAR result tab.
Run Fast Lane when you want the broader fast library. The button may show 96 total endpoints with 67 slow endpoints deferred for later.
Run Slow Endpoints only after Fast QSAR/Fast Lane when deeper endpoints are needed and you can wait longer.
Run EHS Endpoints when environmental, health, safety, ecotoxicity, persistence, exposure, or physical hazard screening is the main question.
Use Clear QSAR memory before switching molecules, changing representation choice, retrying after a stopped run, or clearing stale partial results.

Main Areas

Area	What to review	When to use it
Model selector	SMILES and SELFIES checkboxes under the Model legend.	Use before running QSAR to choose which representation-specific endpoints are submitted.
Run buttons	Run Fast QSAR (12), Run Fast Lane (96, 67 slow later), Run Slow Endpoints (67), Run EHS Endpoints (46), and Clear QSAR memory.	Use to control endpoint scope, runtime, and cache/retry behavior.
Latest QSAR Run	Completion summary such as active endpoint count, representation mix, and model-library count.	Use to confirm what actually completed before interpreting tabs.
Result tabs	QSAR, SMILES Endpoints, and SELFIES Endpoints with badge counts.	Use to read combined output first, then representation-specific endpoint cards.
Endpoint cards	Endpoint value/class, model confidence, applicability-domain notes, skipped/error status, and health/chemistry grouping.	Use to decide whether an endpoint is strong enough for follow-up.

What The Model Selector Means

The Model box controls the molecular representation used by QSAR endpoints. It does not change the molecule itself; it changes which model-representation lane is requested for the current molecule.

Control	Meaning	When to select it
SMILES	Runs endpoints that use the canonical SMILES representation from the current molecule.	Use for the standard QSAR readout and for most routine screening. Confirm the SMILES is correct before running.
SELFIES	Runs endpoints that use SELFIES, a robust molecular string representation designed to avoid invalid molecule strings.	Use when you want representation-robust evidence, SELFIES-aware endpoint comparison, or later token-hotspot/analog work.
SMILES + SELFIES	Runs both available representation lanes and separates the completed endpoint cards into SMILES and SELFIES tabs.	Use when endpoint confidence matters and you want to see whether both representations point in the same direction. This may take longer and endpoint counts can differ by representation.

Run Buttons And When To Use Them

QSAR is split into lanes so users can get a quick answer first, then expand only when the molecule deserves deeper screening.

Button	Purpose	What to expect
Run Fast QSAR (12)	Runs the priority fast panel first.	Use this first for triage. It should quickly update Latest QSAR Run and produce the first QSAR endpoint cards. In the screenshot example, 12 active endpoints completed from the 209-model library.
Run Fast Lane (96, 67 slow later)	Expands beyond the 12 priority endpoints into the broader fast lane while deferring the slow endpoint set.	Use after Fast QSAR when the compound looks worth deeper review. Expect more endpoint cards and a broader ADME/safety/property profile, but not the full slow panel yet.
Run Slow Endpoints (67)	Runs endpoints marked as slower or deferred.	Use after Fast QSAR/Fast Lane when slow endpoints are needed for a final screening note or when a project decision depends on those endpoints.
Run EHS Endpoints (46)	Runs the environmental, health, and safety endpoint lane.	Use for biodegradation, bioaccumulation, ecotoxicity, exposure, environmental fate, physical hazard, or safety-screening questions. EHS can run separately from the normal fast/slow sequence.
Clear QSAR memory	Clears the latest QSAR run state, cached partial results, reused endpoint results, progress messages, and tab counts.	Use before changing molecule, changing SMILES/SELFIES choices, retrying failed/skipped endpoints, or removing stale results. It does not delete the molecule structure.

How To Read The Result Tabs

The tab badge is a completed-result count, not always the configured endpoint count. Counts can differ because some endpoints are representation-specific, skipped, failed, filtered, or still streaming.

Tab	What it shows	How to use it
QSAR	Combined QSAR result view with all completed, non-skipped endpoint cards from the current run.	Start here. It gives the broad decision-support view across active SMILES and SELFIES outputs.
SMILES Endpoints	Only endpoint cards whose prediction came from the SMILES representation.	Use to inspect the standard representation outputs and compare them with the SELFIES tab when both were selected.
SELFIES Endpoints	Only endpoint cards whose prediction came from the SELFIES representation.	Use to see representation-robust outputs and to support SELFIES hotspot or analog-perturbation interpretation.
Latest QSAR Run	A run summary above the tabs, such as fast panel endpoint count, representation mix, deferred endpoints, and model-library count.	Read this before the tabs so you know which lane completed and whether results are partial, fast-only, EHS-only, or expanded.

What Users Should Expect From Each Lane

Each lane answers a different question. Users should avoid reading the first fast panel as the final answer when slow or EHS endpoints are relevant.

Lane	Best for	User expectation
Fast QSAR	Immediate first-pass triage.	Expect a small set of high-priority endpoint cards. Use it to decide whether the molecule is worth deeper screening.
Fast Lane	Broader but still practical endpoint coverage.	Expect more endpoint groups and a better overall profile while slow endpoints remain deferred.
Slow Endpoints	Deeper endpoint completion after the fast lanes.	Expect longer runtime and additional cards that may be important for borderline compounds.
EHS Endpoints	Environmental and safety-specific screening.	Expect endpoints focused on environmental fate, ecotoxicity, biodegradation, bioaccumulation, and hazard-style interpretation rather than general drug-like triage.

Advanced QSAR Views

Advanced QSAR Views are optional interpretation and optimization panels. Load them only after the main endpoint run is complete and only when you need deeper explanation, chemistry utilities, or decision support.

Advanced view	What it opens	When the user should use it
Visual Analytics	Opens heavier visual interpretation tools such as endpoint profile summaries, SAR contribution hints, molecular clipping/heatmap-style views, property radar, and endpoint-focused analytics.	Use after reading the endpoint cards when you need to explain why a model may be sensitive to a structure region or when you want a visual summary for one endpoint. It is interpretive support, not experimental attribution.
Chemistry Utility	Opens chemistry helper panels such as logD/pH-style utility views and drug-likeness radar summaries derived from the current molecule and QSAR profile.	Use when the question is about chemical behavior behind the predictions, such as ionization/pH context, drug-likeness balance, or descriptor-driven interpretation.
Decision Support	Opens comparison and optimization panels, including original-vs-edited variant SMILES, variant QSAR, endpoint shift comparison, and MPO/Chemryt Score criteria tools.	Use when you want to compare a proposed analog or edited SMILES against the original molecule and tune target-product-profile style criteria.
Hide advanced views	Closes the currently loaded advanced panel while keeping the completed QSAR run and main endpoint tabs available.	Use when you are finished with deeper analysis, want a cleaner page, or want to reduce visual load before reading endpoint cards or switching tabs.

How To Use Advanced Views Safely

Advanced views are designed for interpretation after the main result exists. They should not replace the endpoint cards, confidence notes, applicability-domain notes, or experimental follow-up.

User action	Reason	Expected result
Run QSAR first	Advanced panels need a completed profile. During streaming or partial runs, the module keeps advanced content hidden so the user does not interpret incomplete data.	After the run completes, the Advanced QSAR Views block becomes useful for deeper reading.
Start with endpoint cards	The cards contain the direct model result, confidence, applicability-domain status, and skipped/error notes.	The user understands the model output before opening secondary visual or optimization tools.
Open one advanced view at a time	Each button loads a heavier panel with a different purpose.	The page stays focused and the user can separate visual explanation, chemistry utility, and decision support.
Hide advanced views before changing task	The advanced panel may be tied to the current selected endpoint, current molecule, or edited variant.	The user avoids confusing an old advanced-panel context with a new molecule, representation, or endpoint lane.

SELFIES Token Hotspots

ChemrytIQ - SELFIES Token Hotspots is a model-agnostic perturbation view. It edits valid SELFIES tokens, decodes candidate molecules, runs selected QSAR endpoints, and reports which token changes move endpoint predictions.

Control or output	What it means	How the user should read it
Run SELFIES Hotspots	Starts a SELFIES token perturbation scan for the current molecule and selected endpoint context.	Use after a QSAR run when you want to know which local token edits may improve or worsen a prediction. Expect the page to show progress while candidates are generated and scored.
Filtered SELFIES tokens	Default perturbation mode that focuses on practical token edits instead of every possible edit.	Use for a manageable first pass. It is faster and easier to interpret than a full token-wide scan.
Bioisosteric replacements	Perturbation mode for chemistry-aware replacement ideas.	Use when you want analog-like edits that may preserve medicinal chemistry intent while shifting endpoint risk.
Full molecule - token-wide	Broader coverage mode that scans more SELFIES token positions across the molecule.	Use when the first filtered scan is not enough. Expect more candidates, more runtime, and more review work.
Endpoint movement table	Shows candidate edits and how selected endpoint predictions changed.	Look for edits that consistently improve the endpoint without creating new high-risk signals. Do not act on a single favorable delta without checking validity and applicability.
Map	Maps a selected SELFIES hotspot back onto approximate atoms in the structure.	Use to see where the token edit is likely acting. Atom mapping uses RDKit/MCS attribution and should be treated as approximate.
Map heatmap	Aggregates token perturbation effects into a structure heatmap.	Blue regions summarize beneficial endpoint shifts and red regions summarize harmful shifts. Use it as a design clue, not proof of causal atom attribution.
Clear token map	Clears the current hotspot results and selected token/heatmap context.	Use before changing endpoint focus, rerunning with a different mode, or moving to another molecule.

Similar Compounds With Known Data

Similar Compounds With Known Data is a ChEMBL neighbor reality check. It searches for near-neighbor compounds, computes local Morgan Tanimoto similarity, and summarizes available experimental activity records.

Control or output	What it means	How the user should read it
Similar compounds with known data	Expands the known-data panel for the current molecule.	Use when a QSAR-only call is important enough to check against experimental neighbors.
Run ChEMBL check	Searches ChEMBL similarity neighbors and computes local RDKit.js Morgan similarity.	Use after a valid QSAR result. The check can support or weaken practical confidence depending on how close and how consistent the neighbors are.
Refresh ChEMBL check	Repeats the known-data lookup for the current molecule.	Use if the previous lookup failed, if source data changed, or if you want to reload neighbor evidence after a page-state change.
ChEMBL neighbor table	Shows nearest known-data neighbors, names or ChEMBL IDs, similarity, links, and summarized activity examples where returned.	A close neighbor with conflicting measured activity, unfavorable properties, or concerning known data should lower confidence in a QSAR-only decision.
Known-data source note	Explains whether ChEMBL or PubChem neighbor evidence was returned and whether structural alignment was available.	Use this note to understand limitations. If full substructure alignment is unavailable, rely on table-level evidence and Morgan similarity rather than visual alignment.
Hide known-data check	Collapses the neighbor-evidence panel.	Use once you have captured the evidence or when you want to return to endpoint cards without extra context on screen.

How Hotspots And Known Data Work Together

SELFIES hotspots suggest possible edits; known-data neighbors provide experimental context. Strong decisions should consider both when available.

Situation	Recommended reading	Decision cue
Hotspot suggests an improvement and close ChEMBL neighbors agree	Check whether the improved candidate stays chemically plausible and whether neighbor data supports the same endpoint direction.	This is a stronger design clue, but still needs experimental confirmation.
Hotspot suggests an improvement but known neighbors disagree	Treat the edit as uncertain. Review applicability-domain notes, endpoint confidence, and neighbor assay context.	Do not prioritize the edit without additional evidence.
Known-data neighbor has concerning measured activity	Use the neighbor as a caution even if QSAR output looks favorable.	Lower practical confidence and consider follow-up assays or safer analog directions.
No ChEMBL neighbors returned	Use QSAR cards, applicability-domain notes, and SELFIES hotspot trends, but note the lack of experimental neighbor support.	The result remains model-led and should be validated more carefully.

ML Model / Computation Used

Model or method	What it predicts	Implementation details
Server-side QSAR endpoint models	ADME, toxicity, physicochemical, environmental, and safety endpoint predictions.	The module submits canonical SMILES to QSAR APIs and returns endpoint cards with confidence/applicability context. The inspected package includes ONNX/joblib runtime dependencies; endpoint-specific model artifacts are managed by the QSAR server package.
SELFIES hotspot and analog perturbation workflow	Valid token edits and virtual analog scans for endpoint movement.	SELFIES is used as a safe molecular representation layer; canonical SMILES remain the authority sent into prediction models.

Good Practice

QSAR output is computational decision support, not experimental proof. Confirm key safety, potency, and developability decisions experimentally.

Reference Used

This Tutorial page mirrors the ChemrytIQ reference module: ChemrytIQ-QSAR.