Search Billions of Molecular Fingerprints in Milliseconds
Zilliz Cloud powers molecular similarity search at the scale modern drug discovery demands — comparing chemical fingerprints across billion-compound libraries with sub-10ms latency and built-in support for Tanimoto and Jaccard distance metrics.
Molecular Similarity Search Powered by Zilliz Cloud
Build production-grade cheminformatics applications that search, compare, and rank molecular structures at billion scale using Zilliz Cloud.
Lead Compound Discovery
Search billion-scale compound libraries to find structurally similar molecules to your lead candidates. Accelerate structure-activity relationship analysis and identify optimizable compounds — reducing early-stage drug discovery timelines from weeks to minutes.
Virtual High-Throughput Screening
Build virtual screening pipelines that compare query molecules against entire chemical databases in real time. Surface the most promising candidates for wet-lab validation — without waiting days for brute-force pairwise comparisons.
Toxicity and ADMET Prediction
Enable similarity-based toxicity and ADMET profiling by retrieving structurally analogous compounds with known safety data. Let researchers flag potential risks early in the pipeline — before committing to costly in-vivo studies.
Retrosynthetic Route Planning
Build retrosynthesis tools that search for structurally similar intermediates and known reaction pathways across published compound libraries. Help chemists identify feasible synthesis routes — grounded in real chemical precedent, not guesswork.
Chemical Patent Analysis
Search patent databases by molecular structure to identify prior art, freedom-to-operate conflicts, and competitive filings. Give IP teams the ability to assess chemical novelty across millions of patents — in seconds, not days.
Agrochemical Compound Search
Enable crop science teams to search molecular fingerprint libraries for pesticide, herbicide, and fungicide candidates structurally similar to known actives. Accelerate agrochemical R&D by narrowing candidate pools before synthesis.
Protein and Peptide Similarity
Build search systems that compare protein sequence embeddings and peptide fingerprints at scale. Let biotech teams discover functionally similar biologics across proprietary and public databases — without manual sequence alignment.
Materials Discovery Search
Search molecular and crystal structure databases to find materials with target properties — conductivity, stability, solubility. Accelerate materials science R&D by retrieving structurally similar candidates from millions of known compounds.
Why Zilliz?
Why Cheminformatics Teams Choose Zilliz Cloud
Molecular similarity search at production scale demands more than a research prototype. Zilliz Cloud delivers the throughput, capacity, and precision that pharmaceutical and biotech teams need — searching billions of chemical fingerprints with sub-10ms latency and native support for Jaccard and Tanimoto distance metrics.
100K+QPS
Sustain massive concurrent fingerprint queries across teams
Drug discovery pipelines generate thousands of simultaneous similarity queries — from virtual screening batch jobs to interactive medicinal chemistry tools. Zilliz Cloud sustains 100K+ queries per second with stable p99 latency, so screening campaigns and researcher queries never queue.
10B+Vectors
Index entire commercial compound libraries in one place
Chemical databases like ZINC, PubChem, and Enamine collectively contain billions of compounds. Zilliz Cloud indexes 10B+ molecular fingerprint vectors without sharding complexity — so your team searches the full chemical space, not a sampled subset.
-10xCost
Scale your compound library without scaling your budget
Storing and querying billions of high-dimensional molecular fingerprints gets expensive fast. Zilliz Cloud's vector compression and tiered storage reduce infrastructure costs by 10x compared to self-managed alternatives — making billion-scale cheminformatics accessible to teams of any size.
< 10msLatency
Return similarity results fast enough for interactive workflows
Medicinal chemists need real-time feedback when exploring structure-activity relationships. Zilliz Cloud returns the nearest molecular neighbors in under 10ms — fast enough to power interactive compound browsers, Jupyter notebooks, and automated screening pipelines without noticeable delay.
Built-in Jaccard and Tanimoto distance
Natively supports Jaccard distance — equivalent to Tanimoto coefficient for binary fingerprints — plus Hamming, cosine, and L2 metrics. Run molecular similarity searches with the right metric out of the box.
Automatic and elastic scaling
Automatically scales compute and storage as your compound library and query volume grow — with no capacity planning, index rebuilding, or sharding required during screening campaigns.
Native multi-tenant architecture
Built-in tenant isolation lets multiple research teams, projects, or business units search separate compound collections on the same platform — securely and without noisy-neighbor performance issues.
Ease of use
Go from molecular fingerprint ingestion to production-ready similarity search in minutes. Zilliz Cloud manages the infrastructure so your cheminformatics team focuses on science, not DevOps.
Multi-cloud flexibility
Run on AWS, Azure, or GCP across 30+ regions worldwide — keeping compound data close to your research teams and within your organization's cloud and data residency requirements.
Enterprise-grade reliability and compliance
99.95% SLA with SOC 2, ISO 27001, GDPR, and HIPAA compliance — plus regional failover and BYOC support for regulated pharmaceutical and biotech workloads.
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Resources
Deep dives into molecular similarity search
Guides and tutorials for building cheminformatics applications at scale