title: Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization.
abstract: BACKGROUND
  Visualization of large molecular datasets is a challenging yet important topic utilised in diverse fields of chemistry ranging from material engineering to drug design. Especially in drug design, modern methods of high-throughput screening generate large amounts of molecular data that call for methods enabling their analysis. One such method is classification of compounds based on their molecular scaffolds, a concept widely used by medicinal chemists to group molecules of similar properties. This classification can then be utilized for intuitive visualization of compounds.
  
  
  RESULTS
  In this paper, we propose a scaffold hierarchy as a result of large-scale analysis of the PubChem Compound database. The analysis not only provided insights into scaffold diversity of the PubChem Compound database, but also enables scaffold-based hierarchical visualization of user compound data sets on the background of empirical chemical space, as defined by the PubChem data, or on the background of any other user-defined data set. The visualization is performed by a web based client-server application called Scaffvis. It provides an interactive zoomable tree map visualization of data sets up to hundreds of thousands molecules. Scaffvis is free to use and its source codes have been published under an open source license.Graphical abstract.
authors.affiliation: Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
authors.forename: Jakub
authors.initials: J
authors.lastname: Velkoborsky
authors.affiliation: Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
authors.forename: David
authors.identifier: 0000-0003-4679-0557
authors.initials: D
authors.lastname: Hoksza
keywords: Chemical space; Pubchem; Scaffold; Treemap; Visualization