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All living things are formed mostly of carbon compounds called organic compounds. The category of organic compounds includes both natural and synthetic compounds that contain carbon. Although a single, precise definition has yet to be identified by the chemistry community, most agree that a defining trait of organic molecules is the presence of carbon as the principal element, bonded to hydrogen and other carbon atoms. However, some carbon-containing compounds such as carbonates, cyanides, and...
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Pure substances consist of only one type of matter. A pure substance can be an element or a compound. An element consists of only one type of atom, while a compound consists of two or more types of atoms held together by a chemical bond.
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Pure substances consist of only one type of matter. A pure substance can be an element or a compound. An element consists of only one type of atom, while a compound consists of two or more types of atoms held together by a chemical bond. Elements are classified as atomic or molecular based on the nature of their basic units.
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In most main group element compounds, the valence electrons of the isolated atoms combine to form chemical bonds that satisfy the octet rule. For instance, the four valence electrons of carbon overlap with electrons from four hydrogen atoms to form CH4. The one valence electron leaves sodium and adds to the seven valence electrons of chlorine to form the ionic formula unit NaCl (Figure 1a). Transition metals do not normally bond in this fashion. They primarily form coordinate covalent bonds, a...
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CSgator: an integrated web platform for compound set analysis.

Sera Park1, Yeajee Kwon2, Hyesoo Jung1

  • 1Ewha Research Center for Systems Biology, Department of Life Science, Division of Molecular and Life Sciences, Ewha Womans University, Seoul, Korea.

Journal of Cheminformatics
|March 5, 2019
PubMed
Summary

CSgator is a new tool for analyzing compound sets in drug discovery. It uses Compound Set Enrichment Analysis (CSEA) and Compound Cluster Analysis (CCA) to reveal drug targets and bioactivity insights.

Keywords:
Bioactivity profileBioassayCompound networkCompound set analysisDrug target

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Drug discovery

Background:

  • Drug discovery necessitates analyzing compound sets for target, disease, and bioactivity.
  • Existing methods may lack comprehensive set-wise interpretation capabilities.

Purpose of the Study:

  • Introduce CSgator, a novel analytic tool for batch analysis of compound sets.
  • Enable set-wise interpretation of compounds based on target, bioactivity, disease, and structure.
  • Propose and demonstrate the utility of 'Hit Enriched Assays' for novel insights.

Main Methods:

  • Utilizes Compound Set Enrichment Analysis (CSEA) for target and bioactivity profiling.
  • Employs Compound Cluster Analysis (CCA) for structural and functional grouping.
  • Applies CSEA and CCA for batch analysis of compound sets.

Main Results:

  • CSgator provides enriched profiles of targets and bioactivities within compound sets.
  • Identifies potential drug targets and elucidates drug mode-of-action.
  • Demonstrates utility in identifying hidden targets for anti-lymphangiogenesis screening hits through 'Hit Enriched Assays'.

Conclusions:

  • CSgator offers a comprehensive approach for set-wise compound interpretation in drug discovery.
  • The tool facilitates novel insights into drug mechanisms and target identification.
  • The concept of 'Hit Enriched Assays' provides a new perspective for bioassay analysis.