Beast code in Giters

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.

Language:PythonMIT47 7 26

GHOST

Language:Jupyter NotebookMIT44 4 1

EquivariantMultipoleGNN

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

Language:Jupyter NotebookMIT28 2 4

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.

Language:PythonMIT27 3 26

overlapping_assays

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

Language:Jupyter NotebookMIT2500

lightweight-registration

Language:Jupyter NotebookMIT2100

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.

Language:PythonMIT17 5 1

molecular_time_series

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

Language:Jupyter NotebookMIT16 10

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.

Language:PythonMIT16 3 88

customETKDG

Language:Python11 6 1

EnergyBasedClustering

Implementation of Energy Based Clustering

Language:Jupyter NotebookMIT11 2 1

irsa

Language:PythonMIT9 3 3

GNNParametrizedFF

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

Language:PythonMIT8 3 1

cpeptools

Language:PythonMIT7 30

DASH-tree

Partial Charge assignment for Molecular Dynamics

Language:PythonMIT7 10

GNNImplicitSolvent

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

Language:Jupyter NotebookMIT-0700

mdfptools

Language:Jupyter NotebookMIT7 3 4

vsCNN

A C++ and Python implementation of the volume-scaled common nearest neighbor clustering algorithm

Language:C++MIT5 20

msms_wrapper

Small python wrapper for the msms program

Language:GLSLMIT3 20

cadd_exercises

Exercises from TeachOpenCADD for the ETH Intro to CADD course

Language:Jupyter Notebook200

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

Language:Jupyter NotebookMIT2 30