Biological and Medicinal Chemistry

ChemPlot, a Python library for chemical space visualization

Authors

  • Murat Cihan Sorkun Dutch Institute for Fundamental Energy Research & Center for Computational Energy Research & Eindhoven University of Technology ,
  • Dajt Mullaj Dutch Institute for Fundamental Energy Research & Center for Computational Energy Research & Eindhoven University of Technology ,
  • J. M. Vianney A. Koelman Dutch Institute for Fundamental Energy Research & Center for Computational Energy Research & Eindhoven University of Technology ,
  • Süleyman Er Dutch Institute for Fundamental Energy Research & Center for Computational Energy Research

Abstract

Visualizing chemical spaces streamlines the analysis of molecular datasets by reducing the information to human perception level, hence it forms an integral piece of molecular engineering, including chemical library design, high-throughput screening, diversity analysis, and outlier detection. We present here ChemPlot, which enables users to visualize the chemical space of molecular datasets in both static and interactive ways. ChemPlot features structural and tailored similarity methods, together with three different dimensionality reduction methods: PCA, t-SNE, and UMAP. ChemPlot is the first visualization software that tackles the activity/property cliff problem by incorporating tailored similarity. With tailored similarity, the chemical space is constructed in a supervised manner considering target properties. Additionally, we propose a metric, the Distance Property Relationship score, to quantify the property difference of similar (i.e. close) molecules in the visualized chemical space. ChemPlot can be installed via Conda or PyPi (pip). Its web application is freely accessible at https://www.amdlab.nl/chemplot/.

Content

Thumbnail image of Chemplot_a_python_library_for_chemical_space_visualization.pdf

Supplementary weblinks

ChemPlot GitHub Code Repository
The code repository of ChemPlot.
ChemPlot Web Application
A web interface for using ChemPlot without the need for coding expertise.
ChemPlot User Manual
A user manual that contains detailed information and practical examples.