MadFast Similarity Search
Blazing fast similarity searching tools
MadFast is a high-end toolkit for ultra fast chemical similarity search using in-memory data storage and optimized multi threaded-implementation. The outstanding search performance extends the chemical space available for live search to hundreds of millions of compounds. Rapid fingerprint generation and short initialization time, along with the large set of comparison methods, provide you with the possibility to optimize the similarity space. MadFast is a Java application that is available via versatile interfaces: command line, REST API and Web UI. Extensive documentation and usage examples are provided.
MadFast development is driven by user feedback. We are interested in your related workflows, feature requests and use-cases. If you have any comment, question or suggestion please feel free to contact us at firstname.lastname@example.org
Real time similarity search
Visualization of the similarity search results with Web UI let you experience the real time responsiveness during similarity searching of large number of structures.
Think big! MadFast delivers 40 most similar structure in
- ~80 ms per 16 M structures (using 1024 bit binary fingerprints on an Amazon r3.8xlarge machine)
- ~5 sec per 1 billion structures (on the same machine)
- 250-350 MB of memory usage per million molecules (using 1024 bit binary fingerprints)
- 1 million structures per minute preparation (import) speed.
Ad-hoc focused chemical space analysis
MadFast enables the utilization of various descriptors, descriptor configurations and comparison metrics. The Web UI is designed to display search result sets from multiple data sets with dissimilarity distribution histograms.
Similarity based overlap analysis
Similarity based overlap analysis (full matrix calculation) of large libraries, up to millions of compounds is possible with the fast multi query similarity search implementation.
1M by 1M exhaustive similarity search using 1024 bit binary fingerprint takes
- ~30 minutes on c3.8xlarge AWS instance
- ~8 minutes on x1.32xlarge AWS instance
Interactive visualization of the overlap is coming soon in a later release.