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.
@article{arxiv.1906.06170,
title = {FPScreen: A Rapid Similarity Search Tool for Massive Molecular Library Based on Molecular Fingerprint Comparison},
author = {Lijun Wang and Jianbing Gong and Yingxia Zhang and Tianmou Liu and Junhui Gao},
journal= {arXiv preprint arXiv:1906.06170},
year = {2019}
}