LHRK

ligpargen

ts-dart

TS-DART identifies transition states of protein conformational changes from MD simulations using hyperspherical embeddings in the latent space.

ATRANET

PhosphoinositideParameters

The Melo Lab's development repository for Martini coarse-grain phosphoinositide parameters

PathDetect-SOM

A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)

membrane-curvature

MDAnalysis tool to calculate membrane curvature.

kinetics

Python package for modelling enzyme reactions using Monte carlo sampling from parameter distributions

QupKake

calculate-bilayer-power-spectrum

ost_pymodules

A set of modules for advanced analysis of molecular structures and MD trajectories using the OpenStructure (http://www.openstructure.org) software.

MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

LipidDyn

repository associated to our pipeline for lipid dynamics

pybigsmiles

A leightweight python library for parsing BigSmiles

respac_batch

Simple script to perform RESPAC calculations (including APBS) for coarse-grained protein charge distributions.

practical_cheminformatics_tutorials

Practical Cheminformatics Tutorials

rdeditor

Simple RDKit molecule editor GUI using PySide

CLoNe

Clustering tool for biomolecular structural ensembles and data in general.

dash

A versatile and interactive package for solving crystal structures from powder diffraction data

ffconv

Tool to convert between force-field topology file formats for molecular simulations

COBY

COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3

openff-forcefields

Force fields produced by the Open Force Field Initiative

AutoMD

Easy to get started with molecular dynamics simulation.

UGM_2023

Materials from the 2023 RDKit UGM

TS2CG1.2

TS2CG version 1.2

titratable_martini_tools

tools for dealing with titratable MARTINI

copernicus

Copernicus

making-it-rain

Cloud-based molecular simulations for everyone

openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)