rinikerlab

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

lightweight-registration

molecular_time_series

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

overlapping_assays

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

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.

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.

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.

rinikerlab/lightweight-registration

rinikerlab/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.

rinikerlab/GHOST

rinikerlab/overlapping_assays

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

rinikerlab/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.

rinikerlab/EquivariantMultipoleGNN

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

rinikerlab/GNNImplicitSolvent

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

rinikerlab/molecular_time_series

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

rinikerlab/DASH-tree

Partial Charge assignment for Molecular Dynamics

rinikerlab/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.

rinikerlab/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.

rinikerlab/customETKDG

rinikerlab/EnergyBasedClustering

Implementation of Energy Based Clustering

rinikerlab/irsa

rinikerlab/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.

rinikerlab/GNNParametrizedFF

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

rinikerlab/mdfptools

rinikerlab/msms_wrapper

Small python wrapper for the msms program

rinikerlab/ANA2B

rinikerlab/cadd_exercises

Exercises from TeachOpenCADD for the ETH Intro to CADD course

rinikerlab/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

rinikerlab/macrocycle-ff-validation

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

rinikerlab/MD_and_NMR_Relaxometry

rinikerlab/teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

rinikerlab/HybridTopologyViewer

rinikerlab/C-REMDforFRET

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

rinikerlab/glauconic_acid

rinikerlab/gregs-test-project

rinikerlab/reeds_applications

rinikerlab/reeds_protonation_tautomers