Author Archives: Anna Carbery

Unclear documentation? ChatGPT can help!

The PyMOL Python API is a useful resource for most people doing research in OPIG, whether focussed on antibodies, small molecule drug design or protein folding. However, the documentation is poorly structured and difficult to interpret without first having understood the structure of the module. In particular, the differences between use of the PyMOL command line and the API can be unclear, leading to a much longer debugging process for code than you’d like.

While I’m reluctant to continue the recent theme of ChatGPT-related posts, this is a use for ChatGPT that would have been incredibly useful to me when I was first getting to grips with the PyMOL API.

Continue reading

Retrieving AlphaFold models from AlphaFoldDB

There are now nearly a million AlphaFold [1] protein structure predictions openly available via AlphaFoldDB [2]. This represents a huge set of new data that can be used for the development of new methods. The options for downloading structures are either in bulk (sorted by genome), or individually from the webpage for a prediction.

If you want just a few hundred or a few thousand specific structures, across different genomes, neither of these options are particularly practical. For example, if you have several thousand experimental structures for which you have their PDB [3] code, and you want to obtain the equivalent AlphaFold predictions, there is another way!

If we take the example of the PDB’s current molecule of the month, pyruvate kinase (PDB code 4FXF), this is how you can go about downloading the equivalent AlphaFold prediction programmatically.

  1. Query UniProt [4] for the corresponding accession number – an example python script is shown below:
Continue reading

Women in Computing: past, present and what we can do to improve the future.

Computing is one of the only scientific fields which was once female-dominated. In the 30s and 40s, women made up the bulk of the workforce doing complex, tedious calculations in the fields including ballistics, astrophysics, aeronautics (think Hidden Figures) and code-breaking. Engineers themselves found that the female computers were far more reliable than themselves in doing such calculations [9]. As computing machines became available, there was no precedent set for the gender of a computer operator, and so the women previously doing the computing became the computer operators [10].

However, this was not to last. As computing became commercialised in the 50s, the skill required for computing work was starting to be recognised. As written in [1]:

“Software company System Development Corp. (SDC) contracted psychologists William Cannon and Dallis Perry to create an aptitude assessment for optimal programmers. Cannon and Perry interviewed 1,400 engineers — 1,200 of them men — and developed a “vocational interest scale,” a personality profile to predict the best potential programmers. Unsurprisingly given their male-dominated test group, Cannon and Perry’s assessment disproportionately identified men as the ideal candidates for engineering jobs. In particular, the test tended to eliminate extroverts and people who have empathy for others. Cannon and Perry’s paper concluded that typical programmers “don’t like people,” forming today’s now pervasive stereotype of a nerdy, anti-social coder.”

Continue reading

OPIGlets go Kayaking

The 1st of July was the day that the OPIGlets went kayaking!

Brennan very kindly offered to guide a kayaking session from the Oxford University Canoeing and Kayaking Club (OUCKC). There was great uptake from the group, with 10 members joining for a paddle.

The first task was to find a kayak long enough for Jack’s legs. Once he managed to wedge himself in to the largest kayak available, we moved onto being pushed down the ramp one by one, hoping that this would not lead to an immediate capsize.

Continue reading

IWD 2021 and the Gender Pay Gap

Throughout the pandemic, the statistics on division of childcare and home-schooling responsibilities have been shocking: mothers are taking on 150% more homeschooling than fathers (1), while 71% of working mothers’ furlough applications were rejected (2).  A third of working mothers reported having lost  some or all work due to a lack of childcare during the pandemic, with this figure rising to 44% for  BAME mothers. On top of this, 90% of the UK’s 2 million single parents are women (3). These unequal divisions are threatening to undo decades of progress towards gender equality.

In April 2019, the pay gap between men and women in the UK was 17.3% (4), and at the current rate of gender pay gap reduction, the gap will not be closed until 2052 (5).  The causes of this gap continue to be unequal caring responsibilities,  more women in low-paid work and (illegal) discrimination. BAME women are also subject to the ethnicity pay gap.  While this varies regionally and by ethnicity, in London in 2018 the overall figure was 23% (6).

Continue reading

ProCare: cavity similarity searching and its applications to fragment-based drug design

ProCare [1] is a package developed at the University of Strasbourg which is able to align and score the similarity of protein cavities. The aim is to find ligand binding sites between different proteins that are similar enough to bind the same ligand. The method used in ProCare is designed to look particularly at fragment (~⅓ size of a druglike ligand) binding sites. The aim is to predict potential fragment hits by comparing the cavities of the targets.

Continue reading