In our latest immunoinformatics review, OPIG has teamed up with experienced antibody consultant Dr. Anthony Rees to outline the evidence for BCR/antibody repertoire convergence on common epitopes post-pathogen exposure, and all the ways we can go about detecting it from repertoire gene sequencing data. We highlight the new advances in the repertoire functional analysis field, including the role for OPIG’s latest tools for structure-aware antibody analytics: Structural Annotation of AntiBody repertoires+ (SAAB+), Paratyping, Ab-Ligity, Repertoire Structural Profiling & Structural Profiling of Antibodies to Cluster by Epitope (‘SPACE’).
Continue readingCategory Archives: Publications
Writing Papers in OPIG
I’m dedicating this blog post to something I spend a great deal of my time doing – reading the manuscripts that members of OPIG produce.
As every member of OPIG knows we often go through a very large number of drafts as I inexpertly attempt to pull the paper into a shape that I think is acceptable.
When I was a student I was not known for my ability to write, in fact I would say the opposite was probably true. Writing a paper is a skill that needs to be learnt and just like giving talks everyone needs to find their own style.
Before you write or type anything, remember that a good paper starts with researching how your work fits into existing literature. The next step is to craft a compelling story, whilst remembering to tailor your message to your intended audience.
There are many excellent websites/blogs/articles/books advising how to write a good paper so I am not going to attempt a full guide instead here are a few things to keep in mind.
- Have one story not more than one and not less – when you write the paper look at every word/image to see how it helps to deliver your main message.
- Once you know your key message it is often easiest to not write the paper in the order the sections appear! Creating the figures from the results first helps to structure the whole paper, then you can move on to methods, then write the results and discussion, then the conclusion, followed by the introduction, finishing up with the abstract and title.
- Always place your work in the context of what has already been done, what makes your work significant or original.
- Keep a consistent order – the order in which ideas come in the abstract should also be the same in the introduction, the methods, the results, the discussion etc.
- A paper should have a logical flow. In each paragraph, the first sentence defines context, the body is the new information, the last sentence is the take-home message/conclusion. The whole paper builds in the same way from the introduction setting the context, through the results which give the content, to the discussion’s conclusion.
- Papers don’t need cliff hangers – main results/conclusions should be clear in the abstract.
- State your case with confidence.
- Papers don’t need to be written in a dry/technical style…
- …..but remove the hyperbole. Any claims should be backed up by the evidence in the paper.
- Get other people to read your work – their comments will help you (and unless it’s me you can always ignore their suggestions!)
Peer Review: reviewing as an early career researcher
Peer review is an important component of academic research and publishing, but it can feel like an opaque process, especially for those not directly involved. I am very fortunate to have been able to participate in the peer review of multiple papers, despite being very early in my career, through support from my supervisors and a mentoring program run by Sense about Science with Nature Communications. Here are some of the things I have learned.
Continue readingFragment-to-Lead Successes in 2019
In this blogpost, I want to highlight the excellent work by Jahnke and collaborators. For the past 5 years, they have published an annual perspective covering fragment-to-lead success stories from the previous year. Very helpfully, their work includes a table detailing the hit fragment(s) and lead molecule, together with key experimental results and parameters.
Continue readingGraphical abstracts that spark joy on a gloomy day
Have you ever read a paper just because it had a funny, endearing, or utterly bizarre graphical abstract? Ever since a colleague showed me the ‘Graphical abstracts that I gone and found’ Facebook page, I have definitely come across a few, and I thought I would share some of my favourite ones below. If you enjoy this kind of thing, I strongly suggest visiting their page for more – it makes for a wonderful distraction from pretty much anything. Continue reading
What can you do with the OPIG Antibody Suite? v2.0
Since my last blogpost on this topic back in 2018, OPIG has expanded its range of tools for antibody/BCR analysis. Here is an updated summary of the OPIG antibody databases and immunoinformatics tools.
Continue readingDrug Promiscuity vs Selectivity
In drug discovery, compound promiscuity and selectivity refers to the ability of drug compounds to bind to several different- (promiscuous) or only one main target (selective). An important distinction here is that promiscuity is defined as specific interactions with multiple biological targets (polypharmacology) rather than a number of non-specific targets. At first glance, you might expect drugs to be designed to be as selective as possible, only hitting one biological target necessary to treat the disease and therefore reduce the chance of any side effects. This paradigm of single-target specificity has been challenged over the past two decades. Even between scientists in the drug discovery field, compound promiscuity is still a controversial topic. The field has increasingly paid attention to the topic of polypharmacology and studies have shown many pharmaceutically relevant compounds, including approved drugs to derive their biological activity from polypharmacology [1-3].
Continue readingThe Coronavirus Antibody Database (CoV-AbDab)
We are happy to announce the release of CoV-AbDab, our database tracking all coronavirus binding antibodies and nanobodies with molecular-level metadata. The database can be searched and downloaded here: http://opig.stats.ox.ac.uk/webapps/coronavirus
Continue readingDeLinker – Deep Generative Models for 3D Linker Design
*** Disclaimer: This blog post represents some shameless self-promotion. ***
I am delighted to announce that our most recent work, DeLinker, was recently published in the Journal of Chemical Information and Modeling (link).
TCRBuilder: Multi-state T-cell receptor structure prediction
Hello friends of OPIG,
From my last blopig blog post [link: https://www.blopig.com/blog/2019/10/comparative-analysis-of-the-cdr-loops-of-antigen-receptors/], I summarised our findings that TCR CDRs are more flexible than their antibody counterparts. Because of this observation, we believe that it is more appropriate to represent TCR binding sites using an ensemble of conformations.
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