3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery

Albert J. Kooistra, Márton Vass, Ross Mcguire, Rob Leurs, Iwan J.P. deEsch, Gert Vriend, Stefan Verhoeven*, Chris deGraaf

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


eScience technologies are needed to process the information available in many heterogeneous types of protein-ligand interaction data and to capture these data into models that enable the design of efficacious and safe medicines. Here we present scientific KNIME tools and workflows that enable the integration of chemical, pharmacological, and structural information for: i)structure-based bioactivity data mapping, ii)structure-based identification of scaffold replacement strategies for ligand design, iii)ligand-based target prediction, iv)protein sequence-based binding site identification and ligand repurposing, and v)structure-based pharmacophore comparison for ligand repurposing across protein families. The modular setup of the workflows and the use of well-established standards allows the re-use of these protocols and facilitates the design of customized computer-aided drug discovery workflows.

Original languageEnglish
Pages (from-to)614-626
Number of pages13
Issue number6
Publication statusAccepted/In press - 1 Jan 2017


  • Cheminformatics workflows
  • Ligand design
  • Ligand repurposing
  • Target prediction


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