Blaine H. M. Mooers
Dept of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 97104
Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 97104
Laboratory of Biomolecular Structure and Function, University of Oklahoma Health Sciences Center, Oklahoma City, OK 97104
Biomolecular Structure Core, Oklahoma COBRE in Structural Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 97104

Abstract

Protein crystallography produces most of the protein structures used in structure-based drug design. The process of protein structure determination is computationally intensive and error-prone because many software packages are involved. Here, we attempt to support the reproducibility of this computational work by using Jupyter notebooks to document the decisions made, the code, and selected output. We have made libraries of code templates to ease running the crystallography packages in Jupyter notebooks when editing them with JupyterLab or Colab. Our combined use of GitHub, snippet libraries, Jupyter notebooks, JupyterLab, and Colab will help modernize the computing done by structural biologists.

Keywords

literate programming, reproducible research, scientific rigor, electronic notebooks, JupyterLab, Jupyter notebooks, computational structural biology, computational crystallography, biomolecular crystallography, protein crystallography, biomolecular structure, biomedical research, protein*drug interactions, RNA*drug interactions, molecular graphics, molecular visualization, scientific communication, molecular artwork, computational molecular biophysics

DOI

10.25080/majora-1b6fd038-002

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Copyright © 2021 Blaine H. M. Mooers. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.