Online molecular docking for students — Vina reports in minutes
Molecular docking software in your browser — AutoDock Vina online with Meeko prep. Use a crystal PDB when you have one, or a validated predicted pocket when you do not. SMILES batch docking, PDF reports, and docking simulations without installing Vina locally.
AutoDock Vina online
Molecular docking tool & cloud simulations — no local install
Crystal structure optional
Holo PDB, literature site, or predicted pocket
How-to guides
Concepts, workflows, and report-ready walkthroughs
What this docking service does
Automated rigid-receptor docking for coursework and early-stage research. Review the checklist below before you submit — especially binding-site setup and pose QC.
Setup & validation
Receptor input
PDB ID download or upload your own .pdb. Multi-chain PDBs are supported — select one protein chain per job at review.
Ligand input
Single SMILES or batch screening: one SMILES per line, or import a multi-record .sdf file. Platform cap is 300 ligands/job; your plan sets the batch limit (e.g. Free 3, Student 30, Research 100, Lab 300 — see Pricing).
Review before you run
Two-step flow: validate setup (0 credits), then dock. Catch protein, box, and ligand issues before spending compute.
Ligand precheck
Molecular weight, rotatable bonds, and Meeko TORSDOF with clear warn/reject thresholds for Vina-friendly sizes.
Computational ADMET
RDKit Lipinski, Veber, and QED summaries at validate and in results (local calculation — no external API).
Binding site options
Auto box from co-crystal ligand; apo pocketeer top-3 pocket picker; pocket residue anchors (e.g. 214,226,245); optional custom XYZ box. Warns if the box center is far from the protein.
3D box preview
See receptor + docking box in 3Dmol during review. Apo structures show an explicit disclaimer to compare with literature.
Faster re-validation
Change ligands only? Protein/box validation is cached in your browser session — no PDB re-download.
Docking engine
AutoDock Vina (rigid receptor)
Meeko receptor/ligand prep, dimorphite_dl protonation at job pH (default 7.4), RDKit ETKDG + MMFF94. Fixed Vina settings (exhaustiveness 8, 9 modes).
Parallel batch docking
Jobs with 2+ ligands run up to 4 parallel Vina workers on the server. A single failed ligand does not cancel the rest of the batch.
Co-crystal redock check
When a bound ligand is detected, optional RMSD sanity check vs the crystal pose. On by default for single-ligand jobs; off by default for batch (enable in Advanced).
Optional metals
Preserve selected HETATM records (e.g. ZN, MG) in the cleaned receptor.
Results & deliverables
Top 3 poses per ligand
Best-scoring Vina modes exported as SDF/PDB complexes in the ZIP bundle.
Pose quality & confidence
PoseBusters QC (Pass / Warn / Fail) with basic fallback. Pose confidence text from score gap + QC downgrade rules.
Protein–ligand interactions
PLIP when available; distance-heuristic fallback if PLIP fails. 2D interaction diagram, binding-site overview PNG, and ligand 2D structure PNG.
Binding mode interpretation
English discussion paragraph per ligand from affinity, interactions, and pose separation — shown on the result page and in the PDF.
PyMOL publication render
Optional headless PyMOL ray-traced binding-site PNG (cartoon + sticks). Enable in Advanced options; batch jobs render the best hit only.
Batch screening table
Multi-ligand jobs: sortable table with affinity, pose confidence, QC, and ADMET columns (MW, Lipinski, QED).
Interactive 3D viewer
Inspect protein–ligand complexes and switch between exported poses in the browser.
PDF report & Methods copy
Download a PDF with embedded figures. One-click copy of English Methods text for your manuscript.
Optional AI paper draft
After docking completes, generate a Gemini-assisted Discussion + figure legends draft (+1 credit). Not a substitute for human peer review or expert editing.
Results ZIP (structure bundle)
Download results.zip with poses, complexes, figures, ADMET/interaction JSON, and run_manifest.json — see the ZIP contents breakdown on this page.
What’s in the results ZIP?
Every completed docking job includes a results.zip alongside the on-page report and PDF. Use the ZIP for PyMOL/Chimera, offline tables, and reproducibility — the PDF is a human-readable summary of the same run.
PDF report: affinities, pose QC, interaction figures embedded for printing — not a substitute for the structure files in the ZIP.
Job root (once per run)
- result.json
- Summary of docked ligands, failures, scores, and redock status.
- run_manifest.json
- Reproducibility record: pipeline version, Vina settings, box, pH, receptor chain, warnings.
- receptor_clean.pdb
- Prepared receptor used for docking (rigid, cleaned PDB).
- redock_report.json
- Co-crystal redock RMSD check (single-ligand / when enabled).
Per successfully docked ligand
- poses/{ligand}.sdf
- Top 3 Vina poses as multi-record SDF.
- complexes/{ligand}_complex.pdb
- Protein–ligand complex for 3D viewers.
- ligands/{ligand}/
- Ligand PDBQT, docked PDBQT, and protonated SMILES.
- admet/{ligand}.json
- RDKit Lipinski, Veber, QED, and related flags.
- interactions/{ligand}.json
- PLIP interaction table (or distance-heuristic fallback).
- figures/{ligand}/
- 2D interaction diagram, binding-site overview PNG, ligand 2D structure; optional pymol_binding_site.png if PyMOL was enabled.
Not included
These require external tools, manual work, or a future paid tier — not this automated flow.
Flexible / induced-fit docking
Side chains are kept rigid. No Smina or flexible-receptor workflows.
Covalent or specialized targets
No covalent docking, dedicated metalloprotein protocols, or membrane-protein workflows.
Molecular dynamics or MMPBSA
No automated MD stability plots, MM-GBSA/PBSA, or trajectory analysis (planned as separate tier).
Experimental ADMET or SwissADME
ADMET is computational (RDKit) only — not lab data, not SwissADME web results.
AI pose generation (DiffDock, etc.)
Scoring and poses come from AutoDock Vina only.
Multi-chain receptor docking
One protein chain per job. Select a single chain when the PDB has several.
Human expert review
Fully automated pipeline — no manual structure editing, guaranteed binding affinity, or expert peer review (optional AI text draft is generated, not curated by a scientist).
Computational scores, poses, ADMET, and interactions are model predictions only. Always validate binding modes and drug-likeness with experiments and literature before drawing conclusions in a thesis or paper.
Practical guides for your docking coursework
Walkthroughs that take you from picking a protein structure to writing a methods section — clear enough for lab reports and tight enough for deadlines.
Do you need a crystal structure?
When a holo PDB is required, when an apo structure with a predicted pocket works, and how to explain your choice in the report.
Read articleHow docking works — the essentials
Scoring functions, search algorithms, and rigid-receptor assumptions explained in plain language.
Read articleYour first docking run, step by step
Download a PDB, prepare ligands, run Vina, inspect poses, and draft the methods paragraph for your assignment.
Read articleRun Vina in the cloud
When a browser-based workflow beats a local install — setup, limits, and what to expect on a student budget.
Read articleDocking for toxicology & ADMET reports
Combine docking with in silico ADMET predictions in toxicology-focused coursework.
Read articleA student roadmap to learning docking
A four-week plan covering structures, Vina, visualization, and how to read results critically.
Read articleWho uses Dock?
Built for searches like molecular docking online, AutoDock Vina online, docking software for students, and virtual screening simulations.
Medicinal chemistry & pharmacy
Answer “how to do molecular docking” for SAR sets: batch SMILES, ranked Vina scores, interaction figures for lab reports.
Toxicology & ADMET-focused courses
Dock ligands to a target, then use built-in RDKit ADMET flags and interaction tables to discuss off-target risk and drug-likeness in write-ups.
Biochemistry & structural biology
Explain what molecular docking means in your essay: rigid-receptor Vina, binding affinity, pose quality, and limitations vs experiment.
Online docking vs local install
Skip conda, Meeko, and PyMOL scripting on a laptop — same AutoDock Vina engine, browser workflow, export ZIP + PDF for submission.
Learning molecular docking
Start with our guides on crystal structures, binding sites, and how docking simulations work — then run a free Review setup (0 credits).
Virtual screening & hit lists
Run small-library docking simulations (20–100 ligands), compare ranked poses and affinities, and export CSV/ZIP for screening assignments and lead-prioritization reports.
Trusted by students in med-chem & structural biology
“Our cohort had to dock 30 NSAID analogs in a week. I used Review setup first, then one batch job — got the PDF and pose files the TA actually wanted.”
“I used to spend Sunday nights fixing Meeko on my laptop. Here I pasted SMILES, paid with the Student plan credits, and had PLIP tables for my slides Monday morning.”
“The redock check caught a wrong chain ID before I wasted credits. Failed run refunded automatically when the PDB was corrupt — that saved my budget.”
Dock Credits & Plans
Monthly Credits at the best $/credit for regular use. Higher tiers add concurrent jobs and priority queue. One-time packs available when you need a top-up.
Same docking deliverables on every tier: setup review · Vina (top 3 poses) · pose QC · PLIP · ADMET · PDF/ZIP. Optional PyMOL figures (+0.5 credit/job).
Try it out
Includes
- 1 credits / month
1 Credit/month — try a small docking job. No credit card required.
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All plans include:
How Dock Credits work
Credits pay for each docking run. Subscriptions include monthly Credits; one-time packs are fixed-price bundles you buy separately (see Pricing). Both can sit on the same account.
Credits spent per docking run
When you click Run docking, Credits are deducted from your balance by ligand count — whether those Credits came from Free, a subscription, or a one-time pack. This section is about spending Credits, not one-time pack prices.
One-time packs (Single Run, Screening Pack) are sold at a fixed price for a bundled Credit amount on the Pricing → One-time tab. You are not billed per ligand at checkout — the table below shows how those Credits are used each time you run docking.
- 1–3 ligands: 1 Credit
- 4+ ligands: 1 Credit per 5 ligands, rounded up (4–5 ligands = 1 Credit; 12 ligands = 3 Credits)
- PyMOL publication figures: +0.5 Credit per job (optional)
- Optional AI paper draft (Gemini Discussion + figure legends): +1 Credit, charged separately when you generate it after docking completes
- Example: 25 ligands + PyMOL = 5 + 0.5 = 5.5 Credits
Credits spent per run (reference)
| Ligands | Credits | + PyMOL |
|---|---|---|
| 1 | 1 | 1.5 |
| 2 | 1 | 1.5 |
| 3 | 1 | 1.5 |
| 4 | 1 | 1.5 |
| 5 | 1 | 1.5 |
| 6 | 2 | 2.5 |
| 10 | 2 | 2.5 |
| 12 | 3 | 3.5 |
| 15 | 3 | 3.5 |
| 20 | 4 | 4.5 |
| 25 | 5 | 5.5 |
| 30 | 6 | 6.5 |
| 40 | 8 | 8.5 |
| 50 | 10 | 10.5 |
| 100 | 20 | 20.5 |
PyMOL adds +0.5 Credit per job. AI paper draft is +1 Credit, billed separately after docking. Applies to any Credit balance (Free, subscription, or one-time). Other batch sizes: 1–3 ligands = 1 Credit; 4+ = 1 Credit per 5 ligands (rounded up).
When Credits are charged
- Credits are deducted when you submit a docking job (not when it finishes)
- Subscription Credits are always used first; one-time pack Credits are used only after your subscription balance for the period is exhausted
- Free plan: 1 Credit per calendar month (enough for one 1–3 ligand job without PyMOL); unused Credits do not roll over
- Paid plans: monthly subscription Credits reset at the start of each billing period
Upgrading your subscription
- When you upgrade (e.g. Student → Research), your previous subscription is cancelled automatically — you never keep two paid plans at once
- Unused subscription Credits from the old plan do not carry over; your new plan starts with its full monthly allowance (e.g. Research = 40 Credits)
- One-time pack Credits you bought separately are not removed when you upgrade — they stay in your account until used
Subscription + one-time packs together
- You can buy a subscription and one-time packs — both stay on your account
- One-time packs: Single Run (2 Credits), Screening Pack (8 Credits). Credits are added to your purchased balance and spent per run using the rules above
- One-time pack Credits do not expire with the monthly cycle; subscription Credits reset each billing period (or each calendar month on Free)
- Jobs always spend subscription Credits first, then one-time Credits
- We recommend subscribing or upgrading when you need more monthly usage; one-time packs are always available on the pricing page as an alternative
Service failures & credit refunds
Docking runs on our servers; you pay Credits to run the calculation and receive a report/ZIP. A ligand that does not dock successfully (invalid structure, prep error, no usable pose) is a normal scientific outcome — the job still delivers results and Credits are not refunded. A service failure means our platform could not finish or deliver your report/ZIP (system error, crash, or timeout before delivery). In that case, Credits charged for that job are fully refunded automatically (see Credit history). Batch jobs are charged once at submit for the whole batch; partial ligand outcomes are not partially refunded. Subscription payments are separate from job Credits.
Result storage
Download links for ZIP/PDF results expire after 7 days for all plans. Files are then removed from storage — save your results locally.
Frequently asked questions
Does molecular docking need a crystallized protein structure?
Not always. A holo crystal structure (protein with a co-crystal ligand) is best for defining the binding site and redock checks. For many student projects, an apo structure plus a literature-defined or predicted pocket is acceptable if you state your assumptions clearly.
What is molecular docking?
Molecular docking predicts how a small molecule binds in a protein binding site, producing poses and a score (for example Vina affinity in kcal/mol). It supports hypothesis generation for coursework — not experimental proof of binding.
How does molecular docking work?
The receptor is prepared as a search grid; ligands are placed in the binding box and scored by a search algorithm. AutoDock Vina uses rigid-receptor docking (protein fixed, ligand torsions flexible). Our pipeline uses Meeko for PDBQT prep and documents settings in your PDF report.
What is the best molecular docking software for students?
AutoDock Vina remains the standard for teaching labs (fast, well-cited). Dock runs Vina online so you avoid local install. Alternatives like GNINA or DiffDock add ML scoring but differ in setup and reproducibility — for most assignments, Vina plus clear methods text is what markers expect.
How can I run molecular docking online?
Upload a PDB receptor, enter SMILES or SDF ligands, then click Run docking. You receive results as a ZIP and PDF with poses, interactions, and optional PyMOL figures.
What’s in the results ZIP file?
results.zip is the full deliverable for offline work. At the job root: result.json (summary), run_manifest.json (Vina/box/pH for Methods), receptor_clean.pdb, and redock_report.json when applicable. For each docked ligand: top-3 poses (SDF), protein–ligand complex (PDB), ligand PDBQT files, ADMET and interaction JSON, and PNG figures (2D diagram, overview, ligand 2D; optional PyMOL binding-site render). The PDF report mirrors key tables and figures for printing but does not replace the ZIP structures. See the “What’s in the results ZIP?” section under Features on the home page.
How are Credits calculated for a docking job?
A docking run costs 1 Credit for 1–3 ligands, then 1 Credit per 5 ligands rounded up (4–5 ligands = 1 Credit, 6–10 = 2 Credits, etc.). Optional PyMOL figures add 0.5 Credit per job. Credits are checked when you click Run docking, before the job is queued.
When are Credits charged?
Credits are deducted when you submit a docking job, not when it completes. Refunds apply only when our service fails to deliver your report/ZIP (system error, crash, or timeout) — not when individual ligands simply do not dock successfully.
Is a ligand not docking the same as a service failure?
No. Ligand did not dock means the pipeline ran but that molecule could not be prepared or scored (bad SMILES, prep error, etc.) — that is a normal result you paid to test; Credits are not refunded. Service failure means our platform could not complete or deliver your job (server error, crash, timeout with no report/ZIP). Service failures are fully refunded. A completed batch with some ligands skipped is still a delivered job — no partial refund.
When do I get Credits back?
Only for service failures: our system error, crash, or timeout before any report/ZIP is delivered. Check Dashboard → Credit history for refund entries. Fix inputs and submit again when ready. Ligand-level outcomes (could not dock, weak affinity) are not refunds.
If some ligands in a batch could not dock, do I get Credits back?
No. Credits are charged once at submit for the whole batch. Skipped or non-docking ligands are normal scientific outcomes and are listed in your report — not grounds for a refund. Refunds apply only when the entire job fails on our side with no deliverables.
Subscription Credits vs one-time pack Credits?
Subscription Credits reset each billing period and belong to your current plan. One-time pack Credits (Single Run, Screening Pack) are bought separately, do not expire with the month, and are never removed when you upgrade. When you run a job, subscription Credits are always used first; one-time Credits are used only after subscription Credits for the period are exhausted.
What happens when I upgrade my subscription?
Your previous subscription is cancelled automatically — you never keep two paid plans. Unused subscription Credits from the old plan do not carry over; the new plan starts with its full monthly allowance (e.g. upgrading to Research gives 40 Credits). One-time pack Credits you bought separately are kept. You will be asked to confirm this before upgrading from your dashboard.
What do Student, Research, and Lab plans include?
Student ($12/mo): 10 Credits/month — best $/credit for coursework. Research ($35/mo): 40 Credits/month, 2 concurrent jobs, priority queue. Lab ($99/mo): 150 Credits/month, 5 concurrent jobs. Batch size is gated by Credits (up to 300 ligands/job). All plans include the full docking pipeline. See Pricing for details.
Can I buy Credits without a subscription?
Yes. Single Run ($7.99): 2 Credits. Screening Pack ($19.99): 8 Credits. Credits are spent per run by ligand count; concurrency and queue priority follow your plan tier (see Pricing).
What is your subscription refund policy?
You can cancel a subscription anytime to stop future charges. Past subscription payments are generally non-refundable except where required by law. Docking job Credits are separate: they refund automatically only for service failures (no report/ZIP delivered), not for ligands that did not dock.
How long are results kept?
Result files are stored for 7 days on all plans, then removed. Download your ZIP and PDF before expiry.