Hi! Today, I invite you to discuss some of the recent arXiv preprints: - Automatic Middle-Out Optimisation of Coarse-Grained Lipid Force Fields (Empereur-mot et al.) My short summary: Molecular dynamics (MD) simulation is an important computational method that often helps researchers to understand the behaviour of complex supramolecular systems, especially…

Hello! Recently, there was a new JCIM release (volume 61, issue 6). I like this journal a lot, and, as always, there are some articles that interested me the most. In this short post, I’d like to share the short summaries of these articles with you, and invite you to…

Hey! I’m back again with a new quick hack to speed up your chemoinformatics routine. Let’s say you have a .sdf file and you need to quickly extract the field values associated with each molecule from this file. How would you do it? I recommend opting for this awk command: …

Hi! Today, I invite you to discuss some of the recent arXiv preprints (circa 02.07.2021): - Multimodal Graph-based Transformer Framework for Biomedical Relation Extraction (Pingali et al.; submitted 01.07.2021). My short summary: Nowadays, scientists have access to a large corpus of biomedical publications’ texts. It seems promising to use this…

Hello! As the previous post dealt with the most recent arXiv papers circa 30.06.2021, this one updates you on what’s been published today, 01.07.2021. Now then, let us indulge in some most recent chemoinformatics-related arXiv picks: - A Differentiable Neural-Network Force Field for Ionic Liquids (Montes-Campos et al.; published 30.06.2021). …

Hello! This post starts a series of short notes that aim at providing you with a (hopefully) daily overview of recently posted arXiv.org pre-prints, in some way related to chemoinformatics. The idea is to give a quick description of an interesting paper so that a curious reader could read it…

Hi everybody! A French startup company called IKTOS, centered on using AI for drug discovery, has recently announced a free online conference on the same topic. The conference will take place from 8.06.2021 to 9.06.2021. It will be streamed online on a special web platform, available after registration. The list of confirmed speakers includes Dr. Marwin Segler, Dr. Pat Walters, and Prof. Connor Coley, to name a few. You can register for free using this link: https://hopin.com/events/ai-for-de-novo-drug-design-iktos-conference. The link also provides the full and impressive list of awesome speakers and the schedule of their talks (with titles).

Quick Hacks #3: Counting the number of SMILES strings in a .smi file. Hi there. So, there’s yet another common situation when working with chemoinformatics-related data. Imagine that a colleague sends you a .smi file, and says that there is a SMILES string on each line of this file. He…

Quick Hacks #2: Uniting several .sdf files in a single file. Hello! Today I will tell you a quick recipe for another quite common situation in chemoinformatics-related work. Let’s say you have just downloaded a set of 100 structures from a chemical database. The only problem is that each structure…