Biochemistry

The project provides Python tool-chain and shell scripts for molecular simulation workflows: preparation, running and analysing molecular dynamics (MD) simulations of bio- and organic soft condensed matter.

eQuilibrator is a simple web interface designed to enable easy thermodynamic analysis of biochemical systems

Stochastic simulator of biochemical reactions involving multistate agents.

Mesoscopic stochastic simulator of multi-component multi-state agenrs

Haruspex is a Convolutional Neural Network capable of recognizing and predicting secondary structure elements and nucleotides in Cryo-EM reconstruction density.