rinikerlab's repositories
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.
GNNImplicitSolvent
Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
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".
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
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.
teachopencadd
TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
EnergyBasedClustering
Implementation of Energy Based Clustering
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
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.
GNNParametrizedFF
Repository for the models used in the publication 'Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions'
EquivariantMultipoleGNN
Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.