@rinikerlab
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rinikerlab

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Top repositories

1

lightweight-registration

Jupyter Notebook
57
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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
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3

GHOST

Jupyter Notebook
48
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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.
Python
29
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5

EquivariantMultipoleGNN

Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.
Jupyter Notebook
28
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6

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
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7

molecular_time_series

Code and datasets from the publication https://doi.org/10.1186/s13321-023-00787-9
Jupyter Notebook
18
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8

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
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9

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
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10

DASH-tree

Partial Charge assignment for Molecular Dynamics
Python
15
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11

GNNImplicitSolvent

Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
Jupyter Notebook
14
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12

customETKDG

Python
12
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13

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
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14

EnergyBasedClustering

Implementation of Energy Based Clustering
Jupyter Notebook
11
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15

irsa

Python
9
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16

RDKit_mETKDG

A docker image containing changes applied to the ETKDG conformer generator workflow, with example scripts.
C++
8
star
17

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
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18

cpeptools

Python
7
star
19

mdfptools

Jupyter Notebook
7
star
20

vsCNN

A C++ and Python implementation of the volume-scaled common nearest neighbor clustering algorithm
C++
6
star
21

mlddec

Python
5
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22

cadd_exercises

Exercises from TeachOpenCADD for the ETH Intro to CADD course
Jupyter Notebook
3
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23

msms_wrapper

Small python wrapper for the msms program
GLSL
3
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24

Dynamic_Reweighting_FamilyTree

Supporting Information for the Family Tree of Dynamic Reweighting Algorithms
Jupyter Notebook
3
star
25

ANA2B

Jupyter Notebook
2
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26

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
27

MD_and_NMR_Relaxometry

Jupyter Notebook
2
star
28

HybridTopologyViewer

Python
1
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