Biocyc via PubChem


BioCyc is a collection of 2988 Pathway/Genome Databases (PGDBs). Each PGDB in the BioCyc collection describes the genome and metabolic pathways of a single organism. (as of March 2014) The paper is: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. Nucleic Acids Res. 2014 Jan;42(Database issue):D459-71. doi: 10.1093/nar/gkt1103. Epub 2013 Nov 12. The BioCyc Web site contains many tools for navigating, visualizing, and analyzing these databases, and for analyzing omics data. ZINC uses Biocyc via PubChem. We are grateful to the authors of BioCyc for creating and maintaning this resource, and for allowing us to incorporate it in ZINC.

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Chemical Diversity and Clustering

We assess the chemical diversity of a subset by clustering the molecules. First, we sort ligands by increasing molecular weight. Then, we use the SUBSET 1.0 algorithm ( Voigt JH, Bienfait B, Wang S, Nicklaus MC. JCICS, 2001, 41, 702-12) to progressively select compounds that differ from those previously selected by at least the Tanimoto cutoff, using ChemAxon default fingerprints. The resulting representatives have two interesting properties:

  • 1) Each representative differs from all the others by at least the Tanitmoto cutoff and
  • 2) All the molecules in the subset are within the Tanimoto cutoff of at least one representative.
Thus the representatives can be said to "cover" the chemical space of the subset at a given Tanimoto level. N/A indicates that clustering is pending.

Tanimoto Cutoff Level 60% 70% 80% 90% 100%
Number of Representatives 696 1,220 2,121 3,691 12,529

Physical Property Distributions

We compute the physical properties of each molecule in the subset, and graph them below.   Download Calculated Physical Properties

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