Quickstart: First Job in Under 10 Minutes
Get from zero to scored compounds in five steps. No installation, no configuration - just a modern browser with WebGPU support.
Best starting targets: ACE (metalloenzyme, Platinum tier) or Thrombin (serine protease, Silver tier) are ideal for your first run - they have strong benchmark performance and clearly separated actives vs. decoys.
Step 1: Choose a Demo Target (1 min)
- Click Try Demo in the sidebar, or navigate directly to /demo/run
- You'll see 18 validated DEKOIS2 benchmark targets - each has a prepared receptor, 240 ligands (actives + decoys), and a validated scoring profile
- Pick a target (we recommend ACE or Thrombin for beginners)
- Click Dock & Score
WebGPU will score all 240 ligands in approximately 3 seconds - entirely in your browser. No data leaves your machine.
WebGPU required. Chrome 113+, Edge 113+, or Firefox Nightly with WebGPU enabled. If you see a "WebGPU not available" message, try updating your browser or enabling the chrome://flags/#enable-unsafe-webgpu flag.
Step 2: Understand Your Results (2 min)
After scoring completes, you'll see:
Summary Metrics (top of page)
| Metric | What It Means |
|---|---|
| AUC | Area Under ROC Curve - how well actives rank above decoys. 1.0 = perfect, 0.5 = random. |
| EF1% | Enrichment Factor at 1% - how many actives appear in the top 1% of ranked compounds. |
| Tier | Quality tier based on AUC: Platinum (>0.90), Gold (>0.80), Silver (>0.60), Internal (<0.60). |
Results Table
Each row shows one compound with:
- Rank - position in the sorted list (lower score = better predicted binder)
- Compound ID - ligand identifier from the SDF file
- Score - the weighted composite score
- PQS Verdict - Pose Quality Sanity check: PASS, WARN, or TRASH
- Label - Active (known binder) or Decoy (known non-binder), used for benchmark validation
Click any row to expand the detail panel with five tabs.
Step 3: Explore the Physics (2 min)
Click any compound row to open the detail panel. Five tabs are available:
Score Breakdown
Shows how the final score is computed from weighted energy terms. The bar chart reveals which physics terms dominate - E_coul (electrostatics)? E_disp (dispersion)? E_hb (hydrogen bonds)?
Physics
All 14 individual energy terms displayed with their raw values:
| Term | Physical Meaning |
|---|---|
| E_coul | Coulomb electrostatic energy |
| E_hb | Hydrogen bond energy |
| E_disp | Dispersion (van der Waals attractive) |
| E_rep | Repulsion (steric clash penalty) |
| E_vdw | Combined van der Waals (disp + rep) |
| n_hbonds | Number of hydrogen bonds |
| E_bup | Buried unsatisfied polar penalty |
| E_pi / E_t_stack | Pi-stacking and T-stacking |
| E_cation_pi | Cation-pi interactions |
| E_halogen | Halogen bond energy |
| E_aromatic | Aromatic contact energy |
Reading energy signs: For most terms, more negative = stronger interaction = better binding. The exception is E_rep (repulsion) and E_bup (penalty), where lower magnitude is better.
3D View
Interactive molecular visualization showing the docked pose in the binding pocket. Use your mouse to rotate, zoom, and inspect contacts.
QC Flags
Quality control indicators - clash count, pocket occupancy, and any warnings about the pose.
Interactions
2D contact map showing residue-level interactions with distances in angstroms. Useful for verifying that key pharmacophoric contacts are satisfied.
Step 4: Try Your Own Compound (3 min)
Ready to dock something specific?
- Go to Dock a Compound at /dock
- Enter a SMILES string in the input box - try one of these examples:
| Compound | SMILES |
|---|---|
| Aspirin | CC(=O)Oc1ccccc1C(=O)O |
| Ibuprofen | CC(C)Cc1ccc(cc1)C(C)C(=O)O |
| Caffeine | Cn1c(=O)c2c(ncn2C)n(C)c1=O |
- Select a target from the dropdown
- Click Dock - the server will generate a 3D pose and score it
- View the docked pose and score breakdown in the results panel
Dock vs. Demo: The demo uses pre-generated poses (from Glide) rescored with IsoScore. The Dock tool generates new poses from scratch using IsoPose. Both use the same physics scoring engine.
Step 5: Explore Advanced Tools (2 min)
Workbench
Visit /workbench/ for the full tool catalog:
- IsoPose - Full docking with GPU acceleration (~3 sec/ligand)
- IsoScore - Ultra-fast rescoring (~4,000 lig/sec) for pre-docked poses
- 3D Viewer - Load any receptor PDB, toggle KeyColor isosurface to visualize the scoring field
- Interaction Diagrams - See pre-loaded examples (ACE-Lisinopril contacts)
Profiles Library
Visit /profiles/ to browse 70+ validated scoring profiles organized by target class (Kinase, Protease, GPCR, Nuclear Receptor, etc.). Each profile shows its validated AUC, tier, and recommended use.
Autotune
Visit /workbench/autotune to generate a custom scoring profile for your target - no labeled data required. Upload a receptor PDB and compound library, and Autotune will analyze pocket properties and interpolate from validated reference profiles.
What Next?
| Goal | Where to Go |
|---|---|
| Score a large compound library | IsoScore docs - upload receptor + pre-docked poses |
| Prepare your own receptor | Target Prep docs - 4-step pipeline from PDB to scoring grid |
| Customize scoring for your target | Autotune docs - generate a target-specific profile |
| Understand the scoring physics | Physics Reference - all 14 terms explained |
| Verify our benchmark claims | Reproduce Results - download replication kits |
| Understand data privacy | Security & Privacy - what happens to your data |
Consensus scoring tip: If you already use Glide, GOLD, or AutoDock Vina, export your docked poses as SDF and rescore with IsoScore. Compounds that rank highly in both scoring functions are your highest-confidence hits.