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.
overlapping_assays
Code and datasets from the manuscript "Comparing IC50 or Ki values from different sources is a source of significant noise".
EquivariantMultipoleGNN
Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.
molecular_time_series
Code and datasets from the publication https://doi.org/10.1186/s13321-023-00787-9
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.
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.
GNNImplicitSolvent
Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
EnergyBasedClustering
Implementation of Energy Based Clustering
GNNParametrizedFF
Repository for the models used in the publication 'Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions'
cadd_exercises
Exercises from TeachOpenCADD for the ETH Intro to CADD course
msms_wrapper
Small python wrapper for the msms program
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
teachopencadd
TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
macrocycle-ff-validation
Code and data for the paper "Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents"
C-REMDforFRET
Influence of the fluorophore mobility on distance measurements by gas phase FRET
TorsionAngularBinStrings
(T)orsion (A)ngular (B)in (S)trings: Quantifying flexibility by introducing a discrete vector representation of a conformer's dihedral angles to allow for counting of states.