Toolbox for including enzyme constraints on a genome-scale model.

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.

A container for all enzyme constrained models created by GECKO.

ThermoGravimetric Analysis (TGA) helps in understanding and optimising pyrolysis process.

MATLAB program for microkinetic modeling in catalysis

Prediction of transition time (kinetics) associated with aromatic ring flipping using infrequent metadynamics

Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.

MATLAB script to generate 2D and 3D kinetic shapes

Cellular metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. Methods to detect these regulatory interactions are mostly based on in vitro binding assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data i…

A set of Matlab scripts which can simulate temporal traces of DNA using CTMC

This code package simulates the time evolution of a multi-site electron transfer chain, with quantum yield, energy efficiency, and rate matrices as key outputs. The simulation models the rates and population dynamics of multi-step hopping with inter-cofactor separations and driving forces (ΔG) as input parameters.

This repository contains the scripts to analyze data as described in "Probing multiple enzymatic methylatin events in real time with NMR spectroscopy" by ET Usher, et al. Biophys J (2021). 10.1016/j.bpj.2021.09.034