Oxford Protein Informatics Group
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Oxford Protein Informatics Group is a research group in the Department of Statistics at the University of Oxford focusing on aspects of protein modelling, homology modelling, membrane proteins, sequence alignment, antibodies, and drug discovery. Find information on Protein Informatics from Prof. Charlotte M. Deane and her team.
Oxford Protein Informatics Group
5d ago
It is good practice not to commit a data folder to version control if the data is available elsewhere and you do not want to track changes of the data. But do not forget to also add an entry for this folder to .gitignore because otherwise git iterates over all the files in the folder ..read more
Oxford Protein Informatics Group
5d ago
A common measure for the similarity of two molecules is the Tanimoto similarity of their ECFPs (Extended Connectivity FingerPrint). However, there is no clear standard in literature for what kind of ECFPs should be used when calculating the Tanimoto similarity, and that choice can lead to substantially different results. In this post I wish to ..read more
Oxford Protein Informatics Group
5d ago
As a cheminformatician in a drug discovery campaign or an algorithm developer making the perfect Figure 1, when one generates a list of compounds for a given target there is a deep desire that the compounds are well received by the reviewer, be it a med chemist on the team or a peer reviewer. This ..read more
Oxford Protein Informatics Group
1w ago
This July I had the opportunity to be part of the Roche Continents programme [1]. The programme was organised by Roche and LUMA Arles and took place in the beautiful city of Arles in the south of France. Together with 40 students from various disciplines and European universities we discussed and explored the connection between ..read more
Oxford Protein Informatics Group
1w ago
This week, it was my turn to give the short talk at our group meeting. I chose to present a recently published paper on thermostability prediction for nanobodies. The motivation for this work, at least in part, is the need for thermostability in the diverse applications of nanobodies. At OPIG, our research primarily revolves around ..read more
Oxford Protein Informatics Group
1w ago
aka when to use a CutomBuildCommand or a CustomInstallCommand when building python packages with setup.py Bioinformatics software is complicated, and often a little bit messy. Recently I found myself wading through a python package building quagmire and thought I could share something I learnt about when to use a custom build command and when to ..read more
Oxford Protein Informatics Group
1w ago
“For sale: baby shoes, never worn.” ~ Ernest Hemingway?? This is a six-word story famously misattributed to Ernest Hemingway. According to Wikipedia, this story first appeared in 1906, when Hemingway was 7 years old, and later attributed to him in 1991, 30 years after his death. So, no chance it was his. Regardless of its ..read more
Oxford Protein Informatics Group
2w ago
In June, I had the opportunity to visit the Cambridge Crystallographic Data Centre (CCDC) for Science Day to give a lightning talk on my rotation project with OPIG. The day was packed with presentations from researchers and PhD students collaborating with the CCDC, offering a great opportunity to hear about some of the fascinating work ..read more
Oxford Protein Informatics Group
2w ago
Memory management is a key concern when working with large datasets. Many researchers and developers will load entire datasets into memory for processing. Although this is a straightforward approach that allows for quick access and manipulation of data, it has its drawbacks. When the dataset size approaches or exceeds the available physical memory, performance degrades ..read more
Oxford Protein Informatics Group
3w ago
This week (2024-08-07) instead of our usual group meeting, OPIG took to the high seas. The OPIGlets pooled our resources and procured punts from many different berths. Organised by Admiral Nele, we departed from the Cherwell boathouse and shipped out the 0.5 nautical miles (3.28801867e-6 light seconds for those playing along in metric) upriver to ..read more