Tinker: Software Tools for Molecular Design

An interoperable Python framework for biomolecular simulation.

An open source Python framework for transition interface and path sampling calculations.

Code and resources for the EPSRC BioSimSpace project.

Sire Molecular Simulations Framework

Tinker-GPU: Next Generation of Tinker with GPU Support

A bare metal Python library for building and manipulating protein molecular structures

Simulation of cryo-EM ensemble data from atomic models of molecules exhibiting continuous motions

Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.

Python package for calculating configurational entropy from molecular dynamics simulations using the multiscale cell correlation method.

Reveal protein energy centers.

MOLSIM is an interoperable domain ontology designed to semantically represent platform-agnostic biomolecular simulations as FAIR (Findable, Accessible, Interoperable, and Reusable) datasets. This ontology aims to standardize the representation of molecular simulation data, processes, and methodologies across different platforms and tools.

ABC-Laboratory is a prototypical simulation software calculating the fluorescence or absorption of different 'biomolecules'. It uses the Godot Game Engive (v.3) and is the result of my Bachelor Hands-on / internship.

De novo cyclic protein polypeptide design using reinforcement learning.

Python scripts for the application of dissipation-corrected targeted molecular dynamics analysis.

Tools for data generation and data analysis for the eLife research article - "The solubility product extends the buffering concept to heterotypic biomolecular condensates"

A collection of scripts and software to assist with biomolecular simulation in our laboratory

GROMOS Software for (Bio)molecular Simulation: md++ code

GROMOS++ Software for the Analysis of (Bio)molecular Simulation Trajectories