Bio-Otto

Data-science

Collection of useful data science topics along with articles, videos, and code

jax-md

Differentiable, Hardware Accelerated, Molecular Dynamics

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

NeuralPLexer

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

openchat-ui

An open source UI for OpenChat models

baybe

Bayesian Optimization and Design of Experiments

Auto3D_pkg

Auto3D generates low-energy conformers from SMILES/SDF

Complete-Applied-Machine-Learning-with-Projects-Series

This repository contains everything you need to become proficient in Applied Machine Learning

AntiFold

Improved antibody structure-based design using inverse folding

streamlit-condition-tree

A Streamlit component to build a condition tree

MD-IFP

MD trajectory analysis using protein-ligand Interaction Fingerprints

pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

femto

A comprehensive toolkit for predicting free energies

grappa

A Machine Learned Molecular Mechanics Force Field with integration into GROMACS and OpenMM

cgenff_charmm2gmx

Python scripts to convert CGenFF stream files to GROMACS format

Fluorify

Computational fluorine scanning built on OpenMM with Python.

AutoPlate

RShiny app to automate the analysis of 96-well plates such as the fitting of dose-response curves for Pseduotype Micro Neutralisation (pMN) assays

Scripts

Various Python packages and programs - THIS PROJECT IS NO LONGER MAINTAINED

CageCavityCalc

Automated calculation of cavity in molecular cages

py50

Generate Dose-Response Curves in Python

PrinciplesOfDrugDiscovery

Slides from the lecture Principles of Drug Discovery

pyConferenceHelper

collection of scripts that allow you to send emails from python

gromacs_pca_porcupine

Do PCA analysis using Gromace and display by Porcupine plot

mdakit_sasa

Toolkit to calculate the surface accessible area of a molecular dynamic trajectory

openmm-mdanalysis-reporter

MD_project_template

A project template creator mainly focused on Molecular Dynamics simulation and analysis, using conda/mamba and git. Still under active development.

pharmacodynamic-response-models

Collection of pharmacodynamic response models, including dose-response, inhibitor-response, and various receptor-response models that can be fit to response data.

DRC

Fast fitting and plotting of a 4PL-Dose-Response-Curve

py50-streamlit

Streamlit version of py50