On 5th April 2024, over 60 researchers braved the train strikes and gusty weather to gather at Lady Margaret Hall in Oxford and engage in a day full of scientific talks, posters and discussions on the topic of adaptive immune receptor (AIR) analysis!
Short and selfish blog here. Probably been done before, but I shall carry on regardless. I am going to review some metrics relevant to our area of Immunoinformatics. In other words, I will try dissect things such as perplexity, logits, pTM, pLDDT and the ABodyBuilder2 confidence score. These numbers can help inform us on the likelihood of predictions, and whether we should have confidence in them.
Continue readingPandas is one of my favourite data analysis tools working in Python! The data frames offer a lot of power and organization to any data analysis task. Here at OPIG we work with a lot of protein structure data coming from PDB files. In the following article I will go through an example of how I use pandas data frames to analyze PDB data.
Continue readingSimilar to getting lost in a language when moving country, you might encounter a language barrier when moving research fields. This dictionary will guide you in the complex world of immunoinformatics, with a focus on antibodies. Whether your main research will be in this field, you want to apply your machine learning model on antibodies, or you just want to understand the research performed in OPIG, this dictionary will get you started.
The Antibody Dictionary:
Affinity maturation: The optimisation process of naive antibodies to memory antibodies such that the antibody is optimised for a specific antigen.
Antibody: (immunoglobulin) a Y-shaped molecule important in the adaptive immune system. A canonical antibody consists of two identical heavy chains and two identical smaller light chains.
Continue readingAs one of the group’s resident nanobody enthusiasts, on the OPIG retreat this year I presented a talk on shark VNARs, their therapeutic potential and how they differ from VHHs. Here are some of the main points covered:
Continue readingThis blogpost is a short notice about recent quality-of-life and feature updates to our Therapeutic Structural Antibody Database (Thera-SAbDab). We hope these changes will make the database more user-friendly and facilitate new analyses…
Continue readingOPIG’s growing immunoinformatics team continues to develop and openly distribute a wide variety of databases and software packages for antibody/nanobody/T-cell receptor analysis. Below is a summary of all the latest updates (follows on from v1.0 and v2.0).
Continue readingThe Observed Antibody Space (OAS) [1,2] is an amazing resource for investigating observed antibodies or as a resource for training antibody specific models, however; its size (over 2.4 billion unpaired and 1.5 million paired antibody sequences as of June 2023) can make it painful to work with. Additionally, OAS is extremely information rich, having nearly 100 columns for each antibody heavy or light chain, further complicating how to handle the data.
From spending a lot of time working with OAS, I wanted to share a few tricks and insights, which I hope will reduce the pain and increase the joy of working with OAS!
Continue readingFrom 19th-22nd February I was fortunate enough to participate in the joint Keystone Symposium on Next-Generation Antibody Therapeutics and Multispecific Immune Cell Engagers, held in Banff, Canada. Now in their 51st year, the Keystone Symposia are a comprehensive programme of scientific conferences spanning the full range of topics relating to human health, from studies on fundamental bodily processes through to drug discovery.
Continue readingOPIG recently celebrated its 20th year; and on 10 January 2023 I gave a talk just a day before the 10th anniversary of BLOPIG’s first blog post. It’s worth reflecting on what’s stayed the same and what’s changed since then.
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