Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches.

By Hanna Eckert, Jürgen Bajorath. Drug Discovery Today, 2007

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mVOC: a database of microbial volatiles (2013, background): “Nevertheless, small structural modifications can change the biological activity of the molecules dramatically (28).”
Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? (2015, background): “Its applications encompass a number of fields, mostly medicinal chemistry-related, such as virtual screening [4].”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “Molecular similarity can be viewed as the distance between molecules in a continuous high-dimensional space of numerical descriptors (Johnson & Maggiora, 1990; Bender & Glen, 2004; Eckert & Bajorath, 2007).”
Molecular fingerprint similarity search in virtual screening. (2015, background): “Similarity in itself is subjective and can be measured and their results interpreted in several ways [6–8].”
Structure-based Systems Biology for Analyzing Off-target Binding (2011, background): “There is a long history in utilizing small molecule similarity to identify off-targets [132].”
Fragment-based QSAR strategies in drug design (2010, background): “functional groups) and the putative amino-acid residues of the macromolecular target, shape complementarity and other entropic effects [6,12-14,26].”