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ana2b

c-remdforfret

Influence of the fluorophore mobility on distance measurements by gas phase FRET

cadd_exercises

Exercises from TeachOpenCADD for the ETH Intro to CADD course

cpeptools

custometkdg

cyclic_peptide_at_interfaces

dash-tree

Partial Charge assignment for Molecular Dynamics

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

dynamic_reweighting_familytree

Supporting Information for the Family Tree of Dynamic Reweighting Algorithms

energybasedclustering

Implementation of Energy Based Clustering

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.

equivariantmultipolegnn

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

ghost

gnnimplicitsolvent

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

gnnparametrizedff

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

gregs-test-project

hybridtopologyviewer

irsa

lightweight-registration

macrocycle-ff-validation

Code and data for the paper "Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents"

md_and_nmr_relaxometry

mdfptools

mlddec

molecular_time_series

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

msms_wrapper

Small python wrapper for the msms program

overlapping_assays

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

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

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.

rdkit_metkdg

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

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.