UCSF

UMBBD

Introduction

Microbial biocatalytic reactions and biodegradation pathways. The paper is: Ellis LB, Wackett LP. (2012) "Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation" Microbial Informatics and Experimentation 2: 1 (4 January 2012). We are grateful to the authors for creating and curating this database and thank them for allowing us to incorporate its structures in ZINC.

Contact Information

Website
http://umbbd.ethz.ch
Email
Not available
Phone
no phone
Fax
no fax

ZINC Subset Overview

Last updated
2013-02-22
Source catalog size
1,319
Number filtered out
172
Upload to PubChem?
No
Purchasability
Not for Sale (Annotated)

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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 112 180 311 460 793

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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