FPScreen: A Rapid Similarity Search Tool for Massive Molecular Library Based on Molecular Fingerprint Comparison
This tool addresses the need for efficient similarity searches in computational biology, though it is incremental as it builds on existing methods like RDKit and MACCS fingerprints.
The authors tackled the problem of performing rapid similarity searches in massive molecular libraries by developing FPScreen, a tool that processes 100 million molecules in under an hour using molecular fingerprint comparisons.
We designed a fast similarity search engine for large molecular libraries: FPScreen. We downloaded 100 million molecules' structure files in PubChem with SDF extension, then applied a computational chemistry tool RDKit to convert each structure file into one line of text in MACCS format and stored them in a text file as our molecule library. The similarity search engine compares the similarity while traversing the 166-bit strings in the library file line by line. FPScreen can complete similarity search through 100 million entries in our molecule library within one hour. That is very fast as a biology computation tool. Additionally, we divided our library into several strides for parallel processing. FPScreen was developed in WEB mode.