MadFast Similarity Search

Blazing fast similarity searching tools
Ad-hoc Simiarity Search
Product Talk
GlaxoSmithKline: Making the virtual real

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

Product Type:application
Interfaces:CLIGUI ( Web )API ( Web services )

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.

Real time similarity search

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.

Ad-hoc focused chemical space analysis

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.


Articles in the library

MadFast Similarity Search

May 10, 2017 - Presentation
MadFast is a new innovative product for blazing fast in-memory similarity searches of large chemical sets – processing compound sets with hundreds of millions of sizes. This presenta…
Author: ()

Escape from 'availability bias' in compound design

Jun 12, 2017 - Poster
Small molecule design is an information demanding activity, since all relevant knowledge is to be accessible within a single space and requires synchronized application of computational m…

Similarity implicated exploration of the fragment galaxy

Mar 8, 2017 - Poster
Fragment space is a marginal subgroup of the druggable universe of chemical entities considering its population. However, it spans astonishingly high number of structures. GDB-13, the lar…

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