For one of OPIG’s short talks, I recently introduced the work done by Kotaro Tsuboyama et al. found in the paper A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. As the name implies, HERO proteins have been found to retain function even after being boiled at 95C and have been found both in Drosophila and human HEK293T cell lines. Whilst it’s not impossible to find proteins which can “survive” 90+ Celsius, these are expected to be the reserve of extremophiles, not found in humans or fruit flies.
Continue readingCategory Archives: Proteins
Coronavirus
A zoonosis is an infectious disease that has jumped from a non-human animal to humans.
The coronavirus disease 2019 (COVID-19) is one such zoonosis, and is caused by severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2, SARS-CoV-2, or 2019-nCoV). This is very similar to the SARS virus that emerged in 2003. Its recent emergence has resulted in a WHO-declared public health emergency of international concern.
Continue readingConference feedback – MABRA workshop “Adaptive immune repertoires and beyond”
Slightly belated, these are our thoughts on the MABRA workshop at the University of Surrey, which five OPIGlegts attended in January 2020.
AutoDock 4 and AutoDock Vina
A recently just-released publication from Ngyuen et al. ing JCIM pointed out that while AutoDock Vina is faster, AutoDock 4 tends to have better correlation with experimental binding affinity.1
[This post has been edited to provide more information about the cited paper, as well as providing additional citations.]
Ngyuyen et al. selected 800 protein-ligand complexes for 47 protein targets that had both experimental PDB structures complexed with a ligand, as well as their associated binding affinity values.
Continue readingXmas proteins
For this Yuletide blog post, I sought long and hard a set of Christmas-related proteins. It is surprisingly difficult mostly because a google search for “Christmas protein” returns festive whey powders.
Continue readingWhat are Hotspots in Structural Biology?
“Hotspot” is one of those extremely versatile words, similar to “model” and “buffer”, which can mean a variety of things depending on context. According to Merriam-Webster, a hotspot is “a place of more than usual interest, activity, or popularity”. This is the most general definition of the concept I could find in a quick search, and the one I find closest in spirit to the way hotspots are perceived in a structural biology context. What this blog post is definitely not about are hotspots as “areas of political, military, or civil unrest” (my experience with them has so far been mostly peaceful), or anything to do with geology, WiFi connections, or forest fires.
However, even within the context of structural biology and structure-based drug design, the word “hotspot” has multiple meanings. In this blog post, I will try to summarise the main ones I have come across, the (sometimes subtle) differences between them, and provide a few useful papers to serve as an entry point for interested readers. Continue reading
NeurIPS 2019: Chemistry/Biology papers
NeurIPS is the largest machine learning conference (by number of participants), with over 8,000 in 2017. This year, the conference will be held in Vancouver, Canada from 8th-14th December.
Recently, the list of accepted papers was announced, with 1430 papers accepted. Here, I will highlight several of potential interest to the chem-/bio-informatics communities. Given the large number of papers, these were selected either by “accident” (i.e. I stumbled across them in one way or another) or through a basic search (e.g. Ctrl+f “molecule”).
Continue readingA collection of prion factoids
It’s been several years since I last presented a talk on prions to OPIG, so I thought a neat way of getting up to date would be to read “The prion 2018 round tables“. What’s the current understanding and are we any closer to determining a structure of PrPSc?
Continue readingA new way of eating too much
Fresh off the pages of Therapeutic Advances in Endocrinology and Metabolism comes a warning no self-respecting sweet tooth should ignore.
“Liquorice is not just a candy,” write a team of ten from Chicago. “Life-threatening complications can occur with excess use.” Hold on to your teabags. Liquorice – the Marmite of sweets – is about to become a lot more sinister.
Continue readingWhen OPIGlets leave the office
Hi everyone,
My blogpost this time around is a list of conferences popular with OPIGlets. You are highly likely to see at least one of us attending or presenting at these meetings! I’ve tried to make it as exhaustive as possible (with thanks to Fergus Imrie!), listing conferences in upcoming chronological order.
(Most descriptions are slightly modified snippets taken from the official websites.)