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Journal of cheminformatics
Apr 08, 2019;11 (1): 29.

TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data.

Dominique Sydow, Andrea Morger, Maximilian Driller, Andrea Volkamer
Author Information
  1. Dominique Sydow: In Silico Toxicology, Institute of Physiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany. ORCID
  2. Andrea Morger: In Silico Toxicology, Institute of Physiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany. ORCID
  3. Maximilian Driller: In Silico Toxicology, Institute of Physiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany. ORCID
  4. Andrea Volkamer: In Silico Toxicology, Institute of Physiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany. andrea.volkamer@charite.de. ORCID
PMID: 30963287 DOI: 10.1186/s13321-019-0351-x

Abstract

Owing to the increase in freely available software and data for cheminformatics and structural bioinformatics, research for computer-aided drug design (CADD) is more and more built on modular, reproducible, and easy-to-share pipelines. While documentation for such tools is available, there are only a few freely accessible examples that teach the underlying concepts focused on CADD, especially addressing users new to the field. Here, we present TeachOpenCADD, a teaching platform developed by students for students, using open source compound and protein data as well as basic and CADD-related Python packages. We provide interactive Jupyter notebooks for central CADD topics, integrating theoretical background and practical code. TeachOpenCADD is freely available on GitHub: https://github.com/volkamerlab/TeachOpenCADD .

Keywords

Cheminformatics Computer-aided drug design Learning Open source Python RDKit Structural bioinformatics Teaching

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Grants

  1. 031A262C/Bundesministerium für Bildung und Forschung
  2. 391684253/Deutsche Forschungsgemeinschaft
  3. 391684253/Deutsche Forschungsgemeinschaft
  4. PhD Scholarship/HaVo-Stiftung
Journal Article
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