Tag Archives: ChatGPT

Checking your PDB file for clashing atoms

Detecting atom clashes in protein structures can be useful in a number of scenarios. For example if you are just about to start some molecular dynamics simulation, or if you want to check that a structure generated by a deep learning model is reasonable. It is quite straightforward to code, but I get the feeling that these sort of functions have been written from scratch hundreds of times. So to save you the effort, here is my implementation!!!

Continue reading

Writing a BLOPIG Post With ChatGPT: A Personal Take on Using AI for Assisted Writing

Disclaimer: I used ChatGPT to improve the writing style of this article, in combination with some personal curation before obtaining a final version.

You’ve probably heard it all already, from ChatGPT writing code and doing proofreading for you to a rap battle between OPIG’s Antibodies and Small Molecules groups, and more.

Whether you like it or not, ChaGPT has unleashed people’s creative side regarding applications and attempts to find shortcuts. Questionable? Absolutely!

In this BLOPIG post, I show how I used ChatGPT to easily write a post summarising some material of my own intellectual property, which I presented as part of my group meeting talk. Mainly, I list some personal thoughts on the ethical concerns around using ChatGPT to assist your writing.

To start off, I passed on content from my own publication draft to ChatGPT, asking to generate a blog post in plain English for BLOPIG. The outcome:

Not bad.

But, it made me realise a number of things:

  • With great power comes great responsibility [Uncle Ben – Spiderman].
    You are responsible for the ethics that go into using ChatGPT. Are you faking expertise? Are you being actually lazy or just being efficient? Think twice (or many more times) if you’re doing the right thing.
  • It can significantly reduce the number of writing iterations but don’t take it at face value.
    Can you actually trust the plain output? No.
    Never take its output as the ground truth, as Large Language Models such as ChatGPT often produce biased writing outputs.
    Keep in mind that whatever you produce as a scientist will be picked up by others, and prone to drive misinformation, if incorrect. It is OK to reduce mechanical iterations, but it’s NOT OK to skip quality control.
  • Be open about it.
    You don’t want to set the wrong example for your colleagues. So, mention if you use it, how you used it, and it is fine to encourage efficiency, but not incentivising a culture of scientific misconduct and plagiarism. Don’t skip the step of producing quality ideas on your own. This is such a concern that publishers like Elsevier have already reacted by publishing guidelines contemplating this possibility. While Nature Springer is working on ways to spot AI-generated outputs.

The bottom line

What are the dos and don’ts of using ChatGPT?

Yes, use it to have fun. Yes, use it to proofread or polish your writing. Yes, use it to summarise your own ideas. No, don’t use it to do the analysis and interpretation of your results. No, don’t copy and paste its direct output into your publication. No, don’t hide that you used it. Finally, NO, you can’t add ChatGPT as a contributing author!