Discover rinikerlab/GNNParametrizedFF Open Source project

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Repository for the models used in the publication 'Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions'

lightweight-registration

Jupyter Notebook

Ensembler

Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method development or to deepen understanding of a broad spectrum of modeling methods, from basic sampling techniques to enhanced sampling and free energy calculations. It is easy to install, fast, increases shareability, comparability, and reproducibility of scientific code developments.

Python

GHOST

Jupyter Notebook

reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

Python

EquivariantMultipoleGNN

Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.

Jupyter Notebook

overlapping_assays

Code and datasets from the manuscript "Comparing IC50 or Ki values from different sources is a source of significant noise".

Jupyter Notebook

molecular_time_series

Code and datasets from the publication https://doi.org/10.1186/s13321-023-00787-9

Jupyter Notebook

restraintmaker

Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation technique with coordinate-based particles). It can be used on a script layer or as an interactive plugin for PyMol. Features are different selection modes and Optimizers to distribute restraints.

Python

PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

Python

DASH-tree

Partial Charge assignment for Molecular Dynamics

Python

GNNImplicitSolvent

Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations

Jupyter Notebook

customETKDG

Python

Physical_Chemistry_Practicum-Molecular_Dynamics_Simulations

This repository is the used for teaching the Physical Chemistry Practicum about Molecular Dynamics (MD) simulations for pharmacy and biology students at ETHZ

Jupyter Notebook

EnergyBasedClustering

Implementation of Energy Based Clustering

Jupyter Notebook

irsa

Python

RDKit_mETKDG

A docker image containing changes applied to the ETKDG conformer generator workflow, with example scripts.

C++

cpeptools

Python

mdfptools

Jupyter Notebook

vsCNN

A C++ and Python implementation of the volume-scaled common nearest neighbor clustering algorithm

C++

mlddec

Python

cadd_exercises

Exercises from TeachOpenCADD for the ETH Intro to CADD course

Jupyter Notebook

msms_wrapper

Small python wrapper for the msms program

GLSL

Dynamic_Reweighting_FamilyTree

Supporting Information for the Family Tree of Dynamic Reweighting Algorithms

Jupyter Notebook

ANA2B

Jupyter Notebook

decapeptides-membrane

Contains the necessary material to reproduce the content of the paper: Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes

Jupyter Notebook

MD_and_NMR_Relaxometry

Jupyter Notebook

HybridTopologyViewer

Python

rinikerlab/GNNParametrizedFF

rinikerlab

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