eva-not

handson-ml3

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.

papermill

📚 Parameterize, execute, and analyze notebooks

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

schnetpack

SchNetPack - Deep Neural Networks for Atomistic Systems

cdhit

Automatically exported from code.google.com/p/cdhit

alphaflow

AlphaFold Meets Flow Matching for Generating Protein Ensembles

fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).

xyz2mol

Converts an xyz file to an RDKit mol object

yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

openmm-tutorial-msbs

OpenMM tutorial for the MSBS course

Sire

Sire Molecular Simulations Framework

physicsml

A package for all physics based/related models

sire

Sire Molecular Simulations Framework

DeepSurf

A surface-based deep learning approach for the prediction of ligand binding sites on proteins

ParaMol

A Package for Parametrization of Molecular Mechanics Force Fields

protons

OpenMM testbed for constant-pH methodologies.

Data-driven-chemistry

cg_openmm

Tools to build coarse grained models and perform simulations with OpenMM

de-stress

DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.

PeptideModels

Code for peptide ligand design with machine learning models.

biosimspace_tutorials

A tutorials suite for BioSimSpace.

CCP5_Simulation_of_BioMolecules

ML-for-Chemistry

ampal

A simple, intuitive and Pythonic framework for representing biomolecular structure.

TensorNet

A high-level deep learning library built on top of PyTorch.

budeff

A Python implementation of the BUDE force field.

ATCP_23_24

TTSCP_L102C_DSB-MBnThz-vs-TTSCP_L102C_DDSB-MBnThz