Frequently Asked Questions

MolDyn is a virtual screening platform. You submit a SMILES string of your query molecule, and we return ranked candidates from a library of 2.6 million molecules in minutes via HTTPS API.

Schrödinger performs physics-based binding simulation — accurate but slow (weeks per target). MolDyn is the first-pass filter: rapidly identifying the best candidates for downstream docking. We complement Schrödinger, we do not replace it.

No. MolDyn runs as a cloud API. You need only an internet connection and an API key.

For standard Cloud SaaS use: no installation needed. One API call and you are screening 2.6 million molecules.

For Enterprise clients requiring local processing of proprietary libraries: contact us to discuss your data residency requirements.

ChEMBL is a public database of bioactive molecules maintained by EMBL-EBI. We use a curated subset of 2,609,637 molecules from ChEMBL 36.

Yes — in two ways.

For standard use: submit your molecules as SMILES strings via the API. Your SMILES are processed in memory on CellsWave servers and immediately discarded after ranking. Nothing is stored.

For large proprietary libraries (1M+ molecules) requiring on-premise processing without transmitting SMILES to our servers: contact us about Enterprise options. For clients with strict data residency requirements, contact us to discuss options.

Custom library upload (SDF format) is available in Professional and Enterprise plans.

Typically 200 ms per query via HTTPS. First query after server startup may take up to 2 seconds (cold start). Subsequent queries are consistently fast.

2,609,637 molecules from ChEMBL 36. Enterprise plan allows adding your proprietary library.

Computer-based molecule selection without a wet lab. Instead of synthesizing and testing thousands of compounds, you first filter them computationally and only test the best candidates in the lab.

No. MolDyn is optimized for small molecules. For antibodies and biologics, use specialized platforms.

A hit is a molecule that shows biological activity against your target in initial assays. MolDyn helps identify hit candidates before wet lab testing.

Yes. Submit the SMILES of a known active compound for your target and receive a ranked list of structurally similar approved molecules that may bind.

No — this is not our focus. For ADMET use SwissADME, pkCSM, or Schrödinger QikProp.

No free plan — we are a B2B platform for professional drug discovery programs. A trial key with 1,000 queries is issued automatically upon registration for technical evaluation.

1. Register at cellswave.com. 2. Receive your API key by email. 3. POST to api.cellswave.com/v1/screen. Full documentation at cellswave.com/docs.

Currently HTTPS API only. A dashboard is on the roadmap. The API enables full automation into your existing pipeline.

Any language. We provide examples for Python, R, and curl. Standard REST JSON API.

A Python SDK is in development. Meanwhile use the requests or httpx libraries. The example in our docs is 5 lines of code.

Yes. Contact [email protected] with your institutional email to discuss academic pricing.

Starter 99%, Professional 99.5%, Enterprise 99.9% with custom SLA.

Simplified Molecular Input Line Entry System — a text format for molecular structure. Example for aspirin: CC(=O)Oc1ccccc1C(=O)O. Any chemistry package (RDKit, ChemDraw) can export SMILES.

A 4-letter code for a protein structure in the RCSB PDB database. Example: 6LU7 is COVID-19 Mpro. Used with the /v1/dock endpoint.

/v1/screen is ligand-based screening — you provide a query SMILES and receive similar molecules from the library. /v1/dock is structure-based — you provide a PDB ID or PDB file and receive molecules that may bind to its active site.

Yes. POST /v1/dock accepts a pdb_content parameter with your PDB file contents directly. RCSB codes are not required.

JSON array with fields: rank, chembl_id, smiles, score.

A proprietary similarity metric relative to your query. Higher score means higher ranked candidate. Use for ranking, not as an absolute binding affinity measure.

top_k parameter accepts 1 to 10,000. We recommend starting with top_k=500 to 1000 for initial analysis.

Currently one SMILES per request. Batch API (list of SMILES in one request) is on the roadmap for Professional plan.

Trial: 1,000 queries. Starter: unlimited (fair use). Professional: unlimited. Enterprise: unlimited with priority.

HTTP header X-API-Key: your-key. Your key is sent by email after registration.

Yes. HTTPS only. HTTP is not supported. TLS 1.3.

Up to 100 heavy atoms. For larger molecules contact us.

HTTP 400 with message: input preprocessing failed.

Yes — in the dashboard (Professional and above). SDF is automatically converted to SMILES and processed as batch.

No — all requests are synchronous and fast. Typical response time is 200 ms. Webhooks are not needed.

Yes. Cloudflare infrastructure ensures continuous availability. Uptime monitoring is active.

Yes. Current version is /v1/. Minimum 90 days notice before any deprecation.

No. REST JSON API only.

MolDyn respects stereochemistry. Different stereoisomers produce different results. Specify correct stereochemistry in your SMILES.

No — the API returns SMILES and scores. Generate 3D coordinates locally via RDKit or OpenBabel.

On the public DUD-E benchmark (Mysinger et al., J. Med. Chem. 2012). All results are reproducible. Full report at cellswave.com/benchmark-report.

Enrichment Factor at 1%. EF@1% = 12.92 means the top 1% of ranked results contains 12.92 times more active molecules than random selection. This is the metric drug discovery teams actually use.

Area Under the ROC Curve. 0.5 = random, 1.0 = perfect. MolDyn achieves 0.782 on HIV-1 protease.

AUROC evaluates the full ranked list. EF@1% evaluates only the top 1% — what actually goes to wet lab. For practical screening EF@1% is more relevant.

HIV-1 Protease EF@1%=12.92, AChE EF@1%=8.93, Glucocerebrosidase EF@1%=9.89, Renin EF@1%=7.36, Thrombin EF@1%=6.62, Trypsin EF@1%=5.60, BACE-1 EF@1%=4.36. Full details at cellswave.com/benchmark-report.

Factor Xa, Factor VIIa, Urokinase (coagulation cascade). Kinases, GPCRs, nuclear receptors, ion channels. Contact us for roadmap updates.

On HIV-1 protease: MolDyn EF@1% = 12.92, Glide SP EF@1% approximately 8-10 (literature). MolDyn is thousands of times faster at comparable accuracy on supported targets.

If your target is in the validated envelope — yes. For confirmation, start with a Proof of Concept. We run a mini-benchmark on your specific target before you commit to a paid plan.

We will tell you honestly. We do not charge for targets outside our validated envelope. Proof of Concept includes a compatibility check.

100% deterministic. Same query produces identical results every time. Important for audit and regulatory requirements.

No neural networks. No training. Deterministic algorithm. No training data required. No domain shift problem.

MolDyn is a hit identification tool, not for regulatory submission. Results must always be validated in wet lab before any submission.

The ChEMBL library is updated with each ChEMBL release (typically annually). Enterprise clients receive advance notice.

Yes. All our benchmark data uses the public DUD-E dataset. Any team can reproduce our results independently.

Directory of Useful Decoys Enhanced. Standard benchmark dataset for virtual screening (Mysinger et al., 2012). Used by all leading vendors to compare methods.

Send a POST request to api.cellswave.com/v1/screen with your API key and SMILES. Full documentation at cellswave.com/docs.

Yes — import requests, POST to api.cellswave.com/v1/screen with your key and SMILES, parse the JSON response. Five lines of code. See cellswave.com/docs.

Get top 1,000 hits from MolDyn, export as SDF via RDKit, import into Schrödinger Glide for docking. MolDyn to Glide is a standard two-stage pipeline.

Yes. Use the KNIME REST node to call MolDyn API. Results are processed by standard KNIME chemistry nodes.

Yes. HTTP Request component plus JSON parser. Contact us for a ready-made protocol.

Yes. The API is designed for automation. Run screening on a schedule, trigger, or from a CI/CD pipeline.

SMILES up to 10,000 characters, PDB content up to 50 MB, top_k up to 10,000.

Standard PDB format. Must contain at least 3 ATOM or HETATM records. Passed as a string in the pdb_content field.

Yes. Use the httr package. POST to api.cellswave.com/v1/screen with your API key header and JSON body.

Convert the JSON response using pandas to_csv in Python. The dashboard (Professional and above) has a Download CSV button.

Yes. Send parallel HTTP requests. The server handles concurrent requests. We recommend no more than 10 parallel requests for Trial and Starter plans.

Request a usage report from [email protected]. A usage dashboard endpoint is in development.

Your trial key with 1,000 queries is the sandbox for technical evaluation before purchasing a plan.

No. MolDyn is a cloud service. For airgapped deployment contact us regarding the Enterprise plan.

New versions are announced at least 90 days before changes. Current /v1/ is supported through at least end of 2027.

No. SMILES are processed in memory and discarded immediately after the query. Only a SHA-256 hash is logged — mathematically impossible to reverse to the original molecule.

Nobody. Automated systems process queries without human involvement. CellsWave engineers have no access to query contents.

Yes. We do not retain personal data beyond what is necessary. A Data Processing Agreement is available upon request.

MolDyn processes molecular data, not patient medical records. Contact us for HIPAA-specific requirements.

Data is processed in the EU. Results are not stored persistently. Logs (hashes only) are in Supabase EU region.

Since we do not store molecules, there is nothing to delete. Logs contain only irreversible SHA-256 hashes.

Yes. TLS 1.3 for all traffic. HTTPS is mandatory. HTTP is not supported.

Always pass your key in the HTTP header, never in the URL. Rotate your key if you suspect compromise by emailing [email protected].

Contact us immediately at [email protected]. We deactivate the old key and issue a new one within one hour.

Enterprise plan includes API security review. Penetration testing by arrangement.

SOC2 is on our roadmap for 2027. Currently DPA plus ToS provide the compliance baseline required by most pharmaceutical clients.

The algorithm runs exclusively on CellsWave servers. Clients receive only results. It is technically impossible to reconstruct the algorithm from API responses.

Yes. Results are yours. We ask that you acknowledge MolDyn by CellsWave in the methods section. Enterprise plan includes co-authorship options.

Yes. We do not disclose our client list and do not inform competitors that you use MolDyn. Standard B2B SaaS practice.

Nothing — we do not store your molecules. Your results remain local with you. Your API key is deactivated.

Proof of Concept $75,000 one-time. Starter $25,000 per month. Professional $50,000 per month. Enterprise $100,000 per month. Partner $20,000 per quarter plus royalty. Full details at cellswave.com/pricing.

MolDyn is a professional drug discovery tool. A trial key with 1,000 queries is issued automatically after registration for technical evaluation.

Yes for Starter and Professional. Enterprise typically uses an annual contract with quarterly payments.

Wire transfer and invoice with NET-30 terms. Flexible terms available for early-stage companies.

Yes. Contact [email protected] with your institutional email.

One target, eight weeks. Full screening of 2.6 million molecules. Top 1,000 ranked hits with scores. Detailed analytical report. Presentation to your team. Recommendations for next steps. 100% credit toward a monthly plan if you convert within 60 days.

Yes. Upgrades take effect immediately. Downgrades take effect at the start of the next billing period.

Proof of Concept includes a compatibility guarantee. If your target is outside our validated envelope we tell you upfront and do not charge.

Starter and Professional are available monthly or annually. Annual contract saves the equivalent of two months. Enterprise minimum is one year.

For early-stage biotech and academic spinouts. Low fixed fee of $20,000 per quarter plus 2 to 5 percent royalty on clinical assets that originate from MolDyn-ranked hits. We earn when you earn.

Yes. A trial key with 1,000 queries is issued automatically at registration. Sufficient for full technical evaluation of the API.

Invoice to your company with NET-30 standard terms. Wire transfer to our bank account.

No penalty for monthly plans. Annual contracts include standard termination provisions in the SOW.

Starter: email support, 24-hour response. Professional: dedicated Slack channel plus weekly call. Enterprise: dedicated engineer plus on-site visits.

Email [email protected]. We respond within 24 hours and are available for calls across all time zones.