Pinned Repositories
customETKDG
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
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's Repositories
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/EquivariantMultipoleGNN
Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.
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/overlapping_assays
Code and datasets from the manuscript "Comparing IC50 or Ki values from different sources is a source of significant noise".
rinikerlab/lightweight-registration
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/molecular_time_series
Code and datasets from the publication https://doi.org/10.1186/s13321-023-00787-9
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/GNNImplicitSolvent
Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
rinikerlab/irsa
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/cpeptools
rinikerlab/DASH-tree
Partial Charge assignment for Molecular Dynamics
rinikerlab/mdfptools
rinikerlab/vsCNN
A C++ and Python implementation of the volume-scaled common nearest neighbor clustering algorithm
rinikerlab/msms_wrapper
Small python wrapper for the msms program
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/MD_and_NMR_Relaxometry
rinikerlab/teachopencadd
TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
rinikerlab/ANA2B
rinikerlab/HybridTopologyViewer
rinikerlab/C-REMDforFRET
Influence of the fluorophore mobility on distance measurements by gas phase FRET
rinikerlab/cyclic_peptide_at_interfaces
rinikerlab/gregs-test-project
rinikerlab/reeds_applications
rinikerlab/reeds_protonation_tautomers