Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

Coarse-graining of large single-cell RNA-seq data into metacells

[TMLR 2023] Simulate time-integrated coarse-grained MD with multi-scale graph neural networks

Martini 3 small-molecule database

The source of the votca-csg and xtp packages

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Sphere-Tree Construction Toolkit (unofficial repository)

The Active Matter Evaluation Package (AMEP) - a Python library for the analysis of particle-based and continuum simulation data of soft and active matter systems

Tools for coarse-grained molecular dynamics simulations using the SPICA force field

Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (bottom-up) and experimental data (top-down)

Collaborative repository to analyse various coarse-graining methods for networks.

SIRAH Force Field

MicMec, the first implementation of the micromechanical model, ever.

Martini 3 small-molecule database

A toolkit for working with coarse-grain systems

A C++ implementation of the Smith - Waterman algorithm. The system consists of 3 different implementations: the one is sequential, while the other two parallelize the execution in a coarse and a fine level respectively, with the use of multithreading.

Mapping small-molecules to Martini 3 coarse-grained representations

Coarse-grained model of titrating peptides interacting with lipid bilayers

Code for the paper "Conditional Normalizing Flows for Active Learning of Coarse-Grained Molecular Representations" (ICML 2024)

Trajectory matching and Bayesian parametrisation to construct coarse-grained force field for polymer systems