Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients

By Xin Chen, C. Reynolds. 2002

192 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

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Citations in the corpus

PubChem3D: Similar conformers (2011, background): “One of these, known as “ Similar Compounds ” , associates a pair of chemical structures if they have a Tanimoto [5-7] similarity of 0.9 or greater when using the PubChem subgraph binary fingerprint [8] and Eq.”
PubChem3D: conformer ensemble accuracy (2013, methodology): “One method in which PubChem evaluates chemical similarity between two molecules is to use a twodimensional (2-D) dictionary-based fingerprint [5] and the Tanimoto equation [6,7]:”
ChemmineR: a compound mining framework for R (2008, methodology): “Both methods use the highly accurate atom pair approach for scoring structural similarities (Carhart et al., 1985; Chen and Reynolds, 2002).”
What Is High-Throughput Virtual Screening? A Perspective from Organic Materials Discovery (2015, background): “…structures should have similar physicochemical In that sense, it is crucial to choose proper measure of distance in a high-dimensional space to logically place molecules in property spaces deﬁned by proper coordinates in high-dimensional visualization for visual mining (73), (76), (77), and (78).”
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis (2012, methodology): “According to our supplementary computation, the average and standard deviation of the 2-D similarity scores between all compound pairs arising from the 10-K set, computed using the PubChem subgraph fingerprint [36] and Tanimoto equation [37-40], were 0.”
ChemMine. A Compound Mining Database for Chemical Genomics1 (2005, methodology): “To perform similarity searches in ChemMine that are not dependent on the licensing restrictions of commercial software applications, we implemented an improved two-dimensional fragmentbased similarity search technique, based on an algorithm suggested by Chen and Reynolds (2002).”
ChemMine tools: an online service for analyzing and clustering small molecules (2011, methodology): “The first employs atom pairs as structural descriptors (37) and the widely used Tanimoto coefficient as a similarity measure (see below for more details).”
Virtual Screening with AutoDock: Theory and Practice (2010, background): “In addition, the ligands may be filtered based on similarity to known actives (such as by calculating ‘Tanimoto coefficients’), particularly if the screen is a second generation screen [47].”