rinikerlab/GHOST rinikerlab/GHOST

  • Stars
    star
    48
  • Rank 594,835 (Top 12 %)
  • Language
    Jupyter Notebook
  • License
    MIT License
  • Created almost 4 years ago
  • Updated over 2 years ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
rinikerlab/GHOST
github

rinikerlab

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

More Repositories

1

lightweight-registration

Jupyter Notebook
57
star
2

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.
Python
50
star
3

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.
Python
29
star
4

EquivariantMultipoleGNN

Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.
Jupyter Notebook
28
star
5

overlapping_assays

Code and datasets from the manuscript "Comparing IC50 or Ki values from different sources is a source of significant noise".
Jupyter Notebook
28
star
6

molecular_time_series

Code and datasets from the publication https://doi.org/10.1186/s13321-023-00787-9
Jupyter Notebook
18
star
7

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.
Python
17
star
8

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.
Python
16
star
9

DASH-tree

Partial Charge assignment for Molecular Dynamics
Python
15
star
10

GNNImplicitSolvent

Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
Jupyter Notebook
14
star
11

customETKDG

Python
12
star
12

Physical_Chemistry_Practicum-Molecular_Dynamics_Simulations

This repository is the used for teaching the Physical Chemistry Practicum about Molecular Dynamics (MD) simulations for pharmacy and biology students at ETHZ
Jupyter Notebook
12
star
13

EnergyBasedClustering

Implementation of Energy Based Clustering
Jupyter Notebook
11
star
14

irsa

Python
9
star
15

RDKit_mETKDG

A docker image containing changes applied to the ETKDG conformer generator workflow, with example scripts.
C++
8
star
16

GNNParametrizedFF

Repository for the models used in the publication 'Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions'
Python
8
star
17

cpeptools

Python
7
star
18

mdfptools

Jupyter Notebook
7
star
19

vsCNN

A C++ and Python implementation of the volume-scaled common nearest neighbor clustering algorithm
C++
6
star
20

mlddec

Python
5
star
21

cadd_exercises

Exercises from TeachOpenCADD for the ETH Intro to CADD course
Jupyter Notebook
3
star
22

msms_wrapper

Small python wrapper for the msms program
GLSL
3
star
23

Dynamic_Reweighting_FamilyTree

Supporting Information for the Family Tree of Dynamic Reweighting Algorithms
Jupyter Notebook
3
star
24

ANA2B

Jupyter Notebook
2
star
25

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
Jupyter Notebook
2
star
26

MD_and_NMR_Relaxometry

Jupyter Notebook
2
star
27

HybridTopologyViewer

Python
1
star