Category Archives: Proteins

ICML 2020: Chemistry / Biology papers

ICML is one of the largest machine learning conferences and, like many other conferences this year, is running virtually from 12th – 18th July.

The list of accepted papers can be found here, with 1,088 papers accepted out of 4,990 submissions (22% acceptance rate). Similar to my post on NeurIPS 2019 papers, I will highlight several of potential interest to the chem-/bio-informatics communities. As before, 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”).

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Journal Club: the Dynamics of Affinity Maturation

Last week at our group meeting I presented on a paper titled “T-cell Receptor Variable beta Domains Rigidify During Affinity Maturation” by Monica L. Fernández-Quintero, Clarissa A. Seidler and Klaus R. Liedl. The authors use metadynamics simulations of the same T-cell Receptor (TCR) at different stages of affinity maturation to study the conformational landscape of the complementarity-determining regions (CDRs), and how this might relate to an increase in affinity. Not only do they conclude that affinity maturation leads to rigidification of CDRs in solution, but they also present some evidence for the conformational selection model of biomolecular binding events in TCR-antigen interactions.

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Electrostatic interactions govern extreme nascent protein ejection times from ribosomes and can delay ribosome recycling

Finishing up a lingering project from your PhD almost a year into your postdoc is a great feeling, especially when it has actually been about 3 years in the making.

Though somewhat outside of the usual scope of activities in OPIG, I encourage you to take a look if the below summary grabs your interest. The full paper and supporting materials (including some movies which took entirely too long to make) can be found at https://pubs.acs.org/doi/abs/10.1021/jacs.9b12264.

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When antibodies go wrong: how antibodies can help viruses infect cells

I’ve been keeping up to date with the latest coronavirus vaccine developments using Derek Lowe’s blog, a resource which I cannot recommend highly enough. A recent post mentioned that vaccines developers are looking out for signs of antibody-dependent enhancement (ADE), which I vaguely remembered from my undergraduate biochemistry days researching an essay on dengue fever. ADE is an interesting immunology phenomenon, and so I thought I’d treat you all to a brief introduction to the issue.

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The 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

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HERO proteins are here to save you (assuming you’re another protein or a fruit fly)

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.

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Coronavirus

A zoonosis is an infectious disease that has jumped from a non-human animal to humans.

A painting by David S. Goodsell showing coronavirus in pink and purple. Secreted mucus (greenish threads) and antibodies (yellow/orange Y-shapes), and several small immune systems proteins (orange) from the lungs’ respiratory cells surround it. © 2020, David S. Goodsell.

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.

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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.

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