Analysis and Display of the Size Dependence of Chemical Similarity Coefficients

By John D. Holliday, Naomie Binti Salim, Martin Whittle, Peter Willett. 2003

148 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Spectroscopy

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Sunghwan Kim
2. Evan E. Bolton
3. Stephen H. Bryant
4. Anita Rácz
5. Dávid Bajusz
6. K. Kollár‐Hunek
7. Károly Héberger
8. Thomas Girke

In Molecular Biology

1. Sunghwan Kim
2. Evan E. Bolton
3. Stephen H. Bryant
4. Károly Héberger
5. Thomas Girke
6. Yiqun Cao
7. Tyler W. H. Backman
8. Shitong Luo

In Spectroscopy

1. Evan E. Bolton
2. Sunghwan Kim
3. Stephen H. Bryant
4. K. Kollár‐Hunek
5. Anita Rácz
6. Dávid Bajusz
7. Károly Héberger
8. Shitong Luo

Citations in the corpus

• ChemMine tools: an online service for analyzing and clustering small molecules (2011, background): “Alternatively, users can choose other similarity coefficients, such as Tversky or Dice (38).”
• PubChem3D: Similar conformers (2011, unknown): “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]:”
• Sum of ranking differences for method discrimination and its validation: comparison of ranks with random numbers (2011, background): “[9], several chemical similarity coefficients were compared for similarity searching or diversity selection of compound collections.”
• Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? (2015, result): “This finding was later corroborated and detailed by Holliday and coworkers [22].”
• 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.”