Packaging with Conda

If you are as happy for the big snake as I am, you have probably wondered how you can create a Conda package with your amazing code. Fear not, in the following text you will learn how to make others go; 

conda install -c coolperson amazingcode

Roughly, the only thing needed to create a Conda package, is a ‘meta.yaml’ file specific for your code. This file contains all the metadata needed to create your package and is highly customizable. While this means the meta.yaml can be written to allow your Conda package to work on any operating system and with any dependencies (doesn’t have to be python) it can be annoying to write from scratch (here is a guide for manually writing this file). Since we just want to create a simple Conda package, we will in this guide avoid fiddling around with the meta.yaml file and instead create the file based on a PyPI package. This will also give you a nice template, if you later need to adapt your meta.yaml file.
Note: Conda packages can also be made from GitHub repositories, which is likely favorable in most cases, but it also requires some manual work on the meta.yaml.

1. Create a PyPI package of your code

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Five Nuggets of Wisdom for Chairing at a Conference

I recently spoke at the Festival of Biologics 2021 conference in Basel (in-person, just in time!), and was lucky enough to be offered the chance to chair a session of talks. As this was the first time I’d ever been asked to do this, I asked Charlotte for some hints to make things go more smoothly. I found her advice very useful, so I thought I’d share it here for other first-time “chairers”!

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New review on BCR/antibody repertoire analysis out in MAbs!

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’).

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A logical brain teaser to derail your afternoon

Brain teasers have a strange power. For many they evoke nothing more than a mild and transient sense of curiosity. But for a certain subset of people they create an irresistible intellectual temptation which even needs to actively be avoided at times as not to completely derail conversations and take over whole afternoons.

For better or worse, I am in the camp of people who are highly susceptible to brain teasers. I just love them too much. More than once in my lifetime I had to ask a friend not to tell me about a particular brain teaser they had heard about because I knew it would inevitably take over my mind and send me down an almost hypnotic spiral of thoughts whose only escape would be finding the solution.

While brain teasers can admittedly turn into ridiculously powerful distractions for some of us, they are not necessarily a waste of time. They have high recreational value and help the mind to enter a playful and creative state. They serve as mental gymnastics to directly train logical thinking skills, and logical thinking is arguably one of the most powerful transferable skills that exists. And last but not least, brain teasers are canonically used nowadays in job interviews at some of the worlds top employers (Google, Facebook, Microsoft, prestigious hedge funds, …).

In this post, I will present one of my favourite brain teasers to see if I can get you hooked. It is a slightly modified and self-contained version of the so-called pirate game. You can find the solution at the end of the page. Enjoy responsibly! Continue reading →

Benchmarks in De Novo Drug Design

I recently came across a review of “De novo molecular drug design benchmarking” by Lauren L. Grant and Clarissa S. Sit where they highlighted the recently proposed benchmarking methods including Fréchet ChemNet Distance [1], GuacaMol [2], and Molecular Sets (MOSES) [3] together with its current and future potential applications as well as the steps moving forward in terms of validation of benchmarking methods [4].

From this review, I particularly wanted to note about the issues with current benchmarking methods and the points we should be aware of when using these methods to benchmark our own de novo molecular design methods. Goal-directed models are referring to de novo molecular design methods optimizing for a particular scoring function [2].

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An A-Z of Oxford

The 2021/2 academic year is now well underway in Oxford, which means a fresh batch of new students getting to grips with some of the bewildering terminology employed here, as well as prospective applicants for next year trying to figure out what on earth a college is and which one they should apply to. As a wizened final year DPhil student I decided to compile an A-Z of Oxford related terms in the hope that someone might find it useful.

A – Ashmolean Museum

Britain’s first public museum, established all the way back in 1678. Home to exhibits covering Ancient Egypt to Modern Art and everything in between.

The Ashmolean Museum of Art and Archaeology | Art UK
The front of the Ashmolean, right in the middle of Oxford City Centre

B – Battels

A termly bill students receive from their college which might cover things like charges for food and accommodation, or fines for not returning books to the library on time.

C – College

The 39 colleges are small educational institutions which together comprise the University of Oxford. Every student is a member of a college, each of which has their own set of facilities, including a dining hall, bar, library and student accommodation. Colleges also have their own student unions, called the Junior Common Room (for undergraduates) and Middle Common Room (for postgraduates), which are excellent places to socialise and meet people studying lots of different subjects.

Aerial view of Oxford, UK, a very well preserved city with one of the most beautiful university campuses I know about.: ArchitecturalRevival
An aerial view of many of the university’s colleges
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Using normalized SuCOS scores.

If you are working in cheminformatics or utilise protein-ligand docking, then you should be aware of the SuCOS score, an open-source shape and chemical feature overlap metric designed by a former member of OPIG: Susan Leung.

The metric compares the 3D conformers of two ligands based on their shape overlap as well as their chemical feature overlap using the RDKit toolkit. Leung et al. show that SuCOS is able to select fewer false positives and false negatives when doing re-docking studies than other scoring metrics such as RMSD or Protein Ligand Interaction Fingerprints (PLIF) similarity scores and performs better at differentiating actives from decoys when tested on the DUD-E dataset.

Most importantly, SuCOS was designed with fragment based drug discovery in focus, where a smaller fragment ligand is elaborated or combined with other fragments to create a larger molecule, with hopefully stronger binding affinity. Unlike for example RMSD, SuCOS is able to quickly calculate an overlap score between a small fragment and a larger molecule, giving chemists an idea on how the fragment elaboration might interact with the protein. However, the original SuCOS algorithm was not normalized and could create scores of > 1 for some cases.

I’ve uploaded a normalised version of the original SuCOS algorithm as a GitHub fork of Susan’s original repository. You can find the normalised SuCOS algorithm here.

Hopefully this is helpful for anyone using the SuCOS algorithm and for all docking enthusiasts who are interested in an alternative way to evaluate their docked poses.

An idea by any other name would smell as sweet.

A blog post about ideas.

Ideation is the formation of an idea, but how do we ideate? 

The route of the word is “to see”, so when we have an idea we see something. In that moment of realization, we hold on to something quite abstract. Some describe it as a click or pattern or insight. This “seeing” is with the mind, however, not the eyes. Idea also implies sentiment or direction – a path one might say. It’s this last point that resonates with me most. When we are lost, in the sea of thoughts, most of the time the consequences are immediate (no consciousness required). However, sometimes we must pause and ideate. Our path, the next step, is unclear. 

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Monty Python

Every now and then I decide to overthink a problem I thought I understood and get confused – last week, it was the Monty Hall problem. 

For those unfamiliar with the thought experiment, the basic premise is that you are on a game show and are presented with three doors. Behind one of the doors is a car, while behind the other two are goats. 

With zero initial information, you make a guess as to which door you think the car is behind (we assume you have enough goats already). Before looking behind your chosen door, the host opens one of the remaining two doors and reveals a goat. The host then asks you if you would like to change your guess. What should you do? 

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Getting the PDB structures of compounds in ChEMBL

Recently I was dealing with a set of compounds with known target activities from the ChEMBL database, and I wanted to find out which of them also had PDB  crystal structures in complex with that target.

Referencing this manually is very easy for cases where we are interested in 2-3 compounds, but for any larger number, using the ChEMBL and PDB web services greatly reduces the number of clicks.

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