Molecular fingerprint similarity search in virtual screening

Adrià Cereto-Massagué; María José Ojeda; Cristina Valls; Miquel Mulero; Santiago Garcia-Vallvé; Gerard Pujadas

doi:10.1016/j.ymeth.2014.08.005

Molecular fingerprint similarity search in virtual screening

Methods. 2015 Jan:71:58-63. doi: 10.1016/j.ymeth.2014.08.005. Epub 2014 Aug 15.

Authors

Adrià Cereto-Massagué¹, María José Ojeda¹, Cristina Valls¹, Miquel Mulero¹, Santiago Garcia-Vallvé², Gerard Pujadas³

Affiliations

¹ Group of Cheminformatics & Nutrition, Biochemistry and Biotechnology Department, Universitat Rovira i Virgili (URV), Campus de Sescelades, N4 Building, 43007 Tarragona, Catalonia, Spain.
² Group of Cheminformatics & Nutrition, Biochemistry and Biotechnology Department, Universitat Rovira i Virgili (URV), Campus de Sescelades, N4 Building, 43007 Tarragona, Catalonia, Spain; Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat, 1, 43204 Reus, Catalonia, Spain.
³ Group of Cheminformatics & Nutrition, Biochemistry and Biotechnology Department, Universitat Rovira i Virgili (URV), Campus de Sescelades, N4 Building, 43007 Tarragona, Catalonia, Spain; Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Avinguda Universitat, 1, 43204 Reus, Catalonia, Spain. Electronic address: gerard.pujadas@urv.cat.

PMID: 25132639
DOI: 10.1016/j.ymeth.2014.08.005

Abstract

Molecular fingerprints have been used for a long time now in drug discovery and virtual screening. Their ease of use (requiring little to no configuration) and the speed at which substructure and similarity searches can be performed with them - paired with a virtual screening performance similar to other more complex methods - is the reason for their popularity. However, there are many types of fingerprints, each representing a different aspect of the molecule, which can greatly affect search performance. This review focuses on commonly used fingerprint algorithms, their usage in virtual screening, and the software packages and online tools that provide these algorithms.

Keywords: Comparison; Data fusion; Fingerprints; Similarity search; Virtual screening.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Algorithms
Computer Simulation*
Drug Discovery / methods
Drug Discovery / trends
Drug Evaluation, Preclinical / methods*
Models, Molecular
Software