Sometimes you just want to quickly move a copy of a script, image or binary from, for example, your local (linux) machine to another (linux) machine. The usual tool would be SCP, but this can get complicated when there are several layers of ssh and sometimes it doesn’t work at all (as is the case for transfers between the Department of Statistics computers and the outside world).
Continue readingProCare: cavity similarity searching and its applications to fragment-based drug design
ProCare [1] is a package developed at the University of Strasbourg which is able to align and score the similarity of protein cavities. The aim is to find ligand binding sites between different proteins that are similar enough to bind the same ligand. The method used in ProCare is designed to look particularly at fragment (~⅓ size of a druglike ligand) binding sites. The aim is to predict potential fragment hits by comparing the cavities of the targets.
Continue readingJournal 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.
Continue readingWhere do OPIGlets come from?
Now you might think the answer to this question is OSOWs, but in fact they come from a wide variety of Undergraduate degrees!
EEGor on Proteins: A Brain-based Perspective on Crowd-sourced Protein Structure Prediction
EEG-based Brain-Computer Interfaces (BCIs) are becoming increasingly popular, with products such as the Muse Headband and g-tec’s Unicorn Hybrid Black taking off, while in the protein folding space, Fold It and distributed/crowd computing efforts like Fold@home, don’t seem to be talked about as much as they once were.
Game-ification is still just as effective a tool to harness human ingenuity as it once was, so perhaps what is needed is a new approach to crowd-folding efforts that can tap into the full potential of the human mind to manipulate and visualise new 3D structures, by drawing inspiration directly from the minds of users…
How COVID-19 affected my (undergrad) masters
The COVID-19 pandemic hit us all in different ways, and this is a short look into how it affected me, a biochemistry undergrad doing my masters project in OPIG.
The first thing that impacted me was the move to working from home. Now you might think that as the group does only computational work that our work might not be too affected by working from home, as all the servers etc. can be accessed remotely. To a certain extent, this is true, it is possible to work from home for starters. Things may well be right as rain for a few people, but it wasn’t for me. I think a lot of people are finding that things take longer when not in the office even under the best circumstances. Technology and equipment can also reduce your productivity quite majorly. Not having a very fast computer (mine is 5 years old and you can tell) or poor chairs that give you backache (living that wooden dining room chair life) are just examples of things that affect your productivity, and also not something most of can do about.
Continue reading10 reasons why LGBT Pride is still necessary
We are starting the LGBT Pride Month, which commemorates the Stonewall Riots (1959). It has rained a lot since that June 51 years ago when a group of transgender, gay, lesbian, and bisexual people rebelled against the police fighting for their rights, inexistent at that time. Fortunately, the situation has changed for the better: in 2011 the UN National Assembly approved the first Human rights, sexual orientation and gender identity resolution, and the difference between sex and gender is not and up to date, 29 different countries recognise same-sex marriage. Therefore, do we still need to celebrate/commemorate/revindicate LGBT Pride? Yes, yes and one thousand times yes. Why? Here I give you only 10 reasons, but it would not be difficult finding 100 more.
Continue readingVisualising macromolecules and grids in Jupyter Notebooks with nglview
If you do most of your work in Jupyter notebooks, it can be convenient to have a quick visualisation tool to view the results of your latest computation from within the notebook, without having to flick between the notebook and your favourite molecule viewer.
I have recently started using NGLview, an IPython/Jupyter widget, to do this. It is based on the NGL viewer, an embeddable webapp for macromolecular visualisation. The nglvew module documentation can be found here, and in addition to handling the usual formats for molecular structure (.pdb, .mol2, .sdf, .pqr, etc.) and map density(.ccp4 and more), it supports visualising trajectories and even making movies.
Continue readingStoring variables in Jupyter Notebooks using %store magic
We’ve all been there. You’ve just run an expensive computation in your Jupyter Notebook and are about to draw those conclusions which will prove that your theories were right all along (until you find the sixteen bugs in your code which render them invalid, but that’s an issue for a different time). Then at the critical moment, your flatmate begins streaming their Lord Of The Rings marathon in 4k and your already temperamental Wi-Fi severs your connection to the department servers in protest, crashing your Jupyter Notebook, leaving your hopes and dreams in tatters.
Continue readingEditors for remote development
The ongoing COVID-19 situation has forced us all to dramatically rethink how we work, with many industries struggling to adjust their on-site procedures to ensure the safety of workers, and many more adapting to support much of their workforce in working from home. As a largely computational research group, we are incredibly fortunate in our ability to carry out most of our work remotely, and our department’s wonderful IT and administrative support staff have enabled a smooth transition to remote working.
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