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METIS: A versatil FDF5 e active learning workflow for optimization of genetic and metabolic networks
Python code that can be used to analyze molecular dynamics simulations of proteins/polymers solvated in water. The first and second hydration shells are calculated, the molecular volume, the partia…
MATLAB functions to create and handle protein allocation models based on the COBRA format
some scripts for analysis of MD and CADD. And some tutorials.
Matlab code for the IPA (or DCA-IPA) described in "Inferring interaction partners from protein sequences", by Anne-Florence Bitbol, Robert S. Dwyer, Lucy J. Colwell, and Ned S. Wingreen, Proc. Natl…
This repository contains code developed during my Master thesis in the field of protein folding. The goal was to predict amino-acid contacts in proteins, based purely on statistical data from multi…
Companion software for "Coevolutionary methods enable robust design of modular repressors by reestablishing intra-protein interactions"
Calculate and visualize epistasis from combinatorial library
Code to analyze the 1.1.3.15 experimental data
https://www.nature.com/articles/s41598-020-74091-z#Tab1
Sample files to accompany the FT's Chart Doctor column
It uses optimisation algorithms to maximise protein solubility with constrained mutation to protein sequence.
The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent func…
Listing of papers about machine learning for proteins.
PyPEF – Pythonic Protein Engineering Framework
A Rosetta-based Python tool for constructing user-defined variant libraries with amino acid insertions, deletions, using loop closure algorithms and energy minimization.
A pymol plugin that makes it easy to compare the difference between two similar protein structures.