Welcome to The New ChemMine

This is the new version of the ChemMine Database that supports chemical genomics research at the Institute for Integrative Genome Biology at UC Riverside. The general purpose cheminformatics tool box, provided by this service in the past, is now available on a separate site: ChemMine Tools. The ChemMine Database itself is a compound mining portal that facilitates drug and agrochemical discovery and chemical genomics screens. This web service is divided into two major functional components:

  1. Compound Database
  2. Screening Database

A detailed tutorial for using ChemMine’s online services is available on the ReadMe page.

Highlighted Subprojects

  1. ChemmineR is an R package for mining drug-like compound and screening data sets. It contains functions for structural similarity searching, clustering of compound libraries with a wide spectrum of algorithms and utilities for managing complex compound data sets.
  2. The EI project aims to build a method for ultra-fast similarity search and clustering. The EI website serves as a demo for this project. It provides an ultra-fast similarity search service and pre-calculated clustering results for over 19 million compounds from the PubChem Compound Database.


  1. Backman T, Cao Y, Girke T (2011) ChemMine Tools: an online service for analyzing and clustering small molecules. Nucleic Acids Res: 39, 486–491. HubMed
  2. Cao Y, Jiang T, Girke T (2010) Accelerated Similarity Searching and Clustering of Large Compound Sets by Geometric Embedding and Locality Sensitive Hashing. Bioinformatics: 26, 953–959. HubMed
  3. Cao Y, Charisi A, Cheng LC, Jiang T, Girke T (2008) ChemmineR: A Compound Mining Framework for R. Bioinformatics: 24, 1733–1734. HubMed
  4. Cao Y, Jiang T, Girke T (2008) A maximum common substructure-based algorithm for searching and predicting drug-like compounds. Bioinformatics: 24, i366–374. HubMed
  5. Science Magazine Netwatch: 309, 2141–2141.
  6. Girke T, Cheng LC, Raikhel N (2005) ChemMine. A compound mining database for chemical genomics. Plant Physiol: 138, 573–577. HubMed.

Please use the Girke et al. (2005) reference for citing ChemMine in publications.


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