Author Archives: Stephanie Wills

Interactive visualization of protein–ligand complexes with Py3Dmol

I recently had a problem where I wanted to provide an interactive visualization of multiple different protein–ligand complexes, requiring minimal setup by the user, allowing them to zoom in and out and change the visualization style, without just providing multiple PDB files or a PyMOL session.

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Atom mapping with RXNMapper

When recently looking at some reaction data, I was confronted with the problem of atom-to-atom mapping (AAM) and what tools are available to tackle it. AAM refers to the process of mapping individual atoms in reactants to their corresponding atoms in the products, which is important for defining a reaction template and identifying which bonds are being formed and broken. This has many downstream uses for computational chemists, such as for reaction searching and forward and retrosynthesis planning1. The problem is that many reaction databases do not contain these mappings, and annotation by expert chemists is impractical for databases containing thousands (or more) data points.

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Ten quick tips for proofreading your work

For my blog post, I thought I’d revisit my dark past on the other side of academic publishing when I worked as a copy editor and proofreader for two years between my undergrad and Masters. During this time, I worked primarily on review papers and news content. While I don’t claim to be a great writer or editor, I thought I’d share some easy tips to help refine your writing and make it more consistent. This is by no means an exhaustive list and probably most of them will already be familiar to you!

1. Consistency is key

I think two of the most important aspects of proofreading are ensuring consistency and using your common sense. For example, instead of agonizing over how you style a word, choose what you think is most appropriate and check that you’ve applied it consistently throughout the text. Check that style matches between the main text, headings, figure legends and footnotes. Some specific things to look for include the following:

  • Capitalization
    • If you’ve capitalized headings, has this been done throughout?
  • Italicization
    • E.g., have you italicized all your mentions of ‘in silico’? 
  • Superscript and subscript
    • E.g., is ‘half-maximal inhibitory concentration (IC50)‘ the same throughout? 
  • Numbers
    • Have you mixed up numerical and spelled-out numbers?  
    • E.g., I drank five cups of coffee and 4 cups of tea. 
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Filtering molecules with long linkers

Recently I was tasked with filtering out ‘stringy’ molecules that were being produced with the fragment merging method I’m working on (that is, molecules with lots of consecutive non-ring bonds that weren’t necessarily caught with my rotatable bond filter). While this is quite a niche/specific task, through this I discovered a couple of RDKit functions that I wasn’t previously aware of but might be helpful for other people regularly looking at small molecules. The demo adapts code from this helpful blogpost on cutting a molecule into rings and linkers from ‘Is life worth living?’ (which is a useful source of cheminformatics wisdom; https://iwatobipen.wordpress.com/2020/01/23/cut-molecule-to-ring-and-linker-with-rdkit-rdkit-chemoinformatics-memo/). Obviously in practice you may be applying lots of different filters to enumerated molecules, but this is just a small example of something I found useful. 

The Jupyter Notebook can be found at: 

https://github.com/stephwills/Demo-removing-stringy-molecules/blob/main/Molecule%20filter.ipynb

Happy coding, 

Steph