t-distributed stochastic neighbor embedding (t-SNE) is a statistical method for visualizing high-dimensional data by giving each datapoint a location in a two or three-dimensional map. Whilst there are
Category: Hints and Tutorials
Tutorials, Hints, Tips and Tricks
An interesting web app that fetches ChEMBL bioactivity data for a target (via UniProt ID), computes molecular descriptors, and trains a simple predictive model (regression, with
Prediction of the metabolism of small molecules is very challenging and so having a variety of different tools is always useful. I’ve previously written Vortex
Another addition to the superb MayaChemTools OpenFECalculateRelativeBindingFreeEnergySepTop.py to calculate Relative Binding Free Energy using a Separated Topologies (SepTop) approach. The script relies on the availability of OpenFE
PROteolysis TArgeting Chimeras (PROTACs) technology provides an alternative to module biological function by specially using the ubiquitin proteasome system to induce degradation of the target
CNotebook provides chemistry visualization for Jupyter Notebooks and Marimo using the OpenEye Toolkits. Import the package and your molecular data will automatically render as chemical
MolView – SMILES Preview is a Visual Studio Code extension that renders SMILES (Simplified Molecular Input Line Entry System) strings as molecular structure diagrams on
At least on a Mac the default place to store Vortex scripts is in the vortex folder ~/vortex/scripts Any folder/scripts you put in the vortex/scripts
There was an interesting publication from the Todd group at UCL on Chemrxiv “Idler Compounds: A Simple Protocol for Openly Sharing Fridge Contents for Cross-Screening”
This morning I tried to print something to my HP LaserJet Pro printer and got an error. A quick search of the HP website suggested