molecules

There are 2 repositories under molecules topic.

BioPandas / biopandas
Working with molecular structures in pandas DataFrames
molecular-structures pandas-dataframe pdb mol2 protein-structure molecules pdb-files drug-discovery computational-biology bioinformatics molecule
Language:Python 679
HannesStark / EquiBind
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
geometry graph-neural-networks proteins protein-structure drug-discovery molecules equivariance
Language:Python 463
datamol-io / datamol
Molecular Processing Made Easy.
python molecule rdkit drug-discovery drug-design molecules cheminformatics medicinal-chemistry
Language:Python 422
dewberryants / asciiMol
Curses based ASCII molecule viewer for terminals.
chemistry cheminformatics molecules visualization ascii
Language:Python 349
jparkhill / TensorMol
Tensorflow + Molecules = TensorMol
tensorflow molecules neural-network chemistry molecular-dynamics molecular-simulation simulation force-field monte-carlo meta-dynamics machine-learning
Language:Python 269
gcorso / torsional-diffusion
Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)
chemistry conformer-generator equivariance geometry machine-learning molecules torsion-angles neurips-2022
Language:Python 232
lucidrains / equiformer-pytorch
Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding
artificial-intelligence deep-learning equivariance transformers attention-mechanisms protein-folding molecules
Language:Python 224
gnn-lspe
vijaydwivedi75 / gnn-lspe
Source code for GNN-LSPE (Graph Neural Networks with Learnable Structural and Positional Representations), ICLR 2022
graph-neural-networks transformers graph-transformer positional-encoding graph-deep-learning transformer-networks attention graphs molecules gnn-lspe lspe graph-representation-learning geometric-deep-learning representation-learning gnn message-passing
Language:Python 221
kjappelbaum / awesome-chemistry-datasets
overview of datasets for ML in chemistry
ai awesome chemistry data hacktoberfest machine-learning molecules
197
pcko1 / Deep-Drug-Coder
A tensorflow.keras generative neural network for de novo drug design, first-authored in Nature Machine Intelligence while working at AstraZeneca.
autoencoders denovo-design drug-discovery lstm-neural-networks molecules neural-network smiles-strings
Language:Python 180
ScaffoldGraph
UCLCheminformatics / ScaffoldGraph
ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.
rdkit networkx scaffold-networks scaffold-trees cheminformatics murcko fragments molecules scaffolds hiers chemistry computational-chemistry
Language:Python 159
HannesStark / 3DInfomax
Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.
graph-representation-learning self-supervised-learning graph molecules 3d pytorch-geometric dgl-graph gnn graph-neural-networks
Language:Python 142
senya-ashukha / simple-equivariant-gnn
A short and easy PyTorch implementation of E(n) Equivariant Graph Neural Networks
graph-neural-networks gnn equivariance pytorch egnn qm9 homo molecules neural-networks deep-learning deep-neural-networks
Language:Python 118
samirelanduk / atomium
Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)
biology proteins structural-biology chemistry molecules
Language:Python 101
aimat-lab / gcnn_keras
Graph convolutions in Keras with TensorFlow, PyTorch or Jax.
graph-convolution ragged-tensors graph-networks graph-algorithms graphs molecules networks machine-learning neural-networks
Language:Jupyter Notebook 96
chao1224 / Geom3D
Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023
3d 3d-structures ai4science biology chemistry crystals drugs equivariance geometry group invariance material molecules physics proteins symmetry
Language:Python 96
virtualramblas / awesome-deep-learning-4-life-sciences
A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).
biotech cheminformatics deeplearning drug-discovery drug-repurposing molecules pharmaceuticals proteins python
82
khavernathy / mcmd
Monte Carlo and Molecular Dynamics Simulation Package
molecular-dynamics-simulation polarization monte-carlo pdb molecular-dynamics chemistry physics physics-simulation monte-carlo-simulation periodicity nvt monte-carlo-simulations molecular-simulation molecules atomic gas-dynamics gas-model crystal-structure crystal xyz
Language:C++ 77
Avogadro / avogadro
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
chemistry linux mac molecules qt visualization windows
Language:C++ 66
PDN
benedekrozemberczki / PDN
The official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)
gcn gnn deepwalk multiplex graph2vec pytorch graph-neural-network deep-learning pathfinder message-passing neural-message-passing cheminformatics molecules graph-classification node-classification network-science data-science transformer bert gpt-3
Language:Python 57
lucidrains / molecule-attention-transformer
Pytorch reimplementation of Molecule Attention Transformer, which uses a transformer to tackle the graph-like structure of molecules
artificial-intelligence deep-learning transformers molecules
Language:Python 56
arpitnarechania / d3-molecule
D3 based interactive visualization library + tool to make render atoms and molecules learning chemical bonding in a fun way.
d3 chemoinformatics molecules atoms-in-molecules chemical-bonding javascript open-source interactive-visualizations
Language:HTML 42
vsomnath / graphretro
Learning Graph Models for Retrosynthesis Prediction (NeurIPS 2021)
retrosynthesis geometry graph-neural-network machine-learning molecules neurips-2021
Language:Python 39
react-native-template
wednesday-solutions / react-native-template
An enterprise react-native template application showcasing - Testing strategy, Global state management, middleware support, a network layer, component library integration, localization, navigation configuration and CI
es6 eslint javascript react react-native apisauce redux reduxsauce saga molecules redux-saga architecture atoms scenes react-native-boilerplate react-native-starter react-native-template
Language:JavaScript 36
PanMig / Chemistry-Lab
A 3D first person serious game, aiming to teach player about molecules through an immersive and fun way.
unity3d serious-game molecules chemistry-lab game
Language:C# 33
lukasturcani / stk-vis
A cross-platform application for visualization of molecular databases.
molecules molecular-structures molecular-modeling chemistry cheminformatics visualization data-visualization database mongodb
Language:PureScript 32
avrabyt / st-speckmol
🧬Streamlit Component for creating Speck molecular structures within Streamlit Web app🚀.
bioinformatics molecules pdb python streamlit streamlit-component visualization
Language:Python 25
alexriss / ChemfilesViewer.jl
Julia library to visualize molecules and other chemical structures
3d chemistry julia julialang molecules render science visualization
Language:Jupyter Notebook 19
SENSAAS / sensaas
Shape-based alignment of molecules using 3D point-based representation
bioinformatics chemicals cheminformatics computational-chemistry drug-design molecular-modeling molecules
Language:Python 16
aacgn / atomic
A JavaScript library for building atomic interfaces with vertical and horizontal micro-frontends
javascript micro-frontend virtual-dom dom-events reactjs angular vuejs micro-frontends single-spa molecules atoms transition-page atomic-template postmessage
Language:JavaScript 15
OpenChemistry / molecules
Common molecule fragments for visualization in Avogadro
molecules common-molecule-fragments chemistry
13
andrewtarzia / mol-ellipsize
Molecular size calculation based on ellipsoid fitting over N conformers
chemistry high-throughput molecular-size molecules rdkit
Language:TeX 12
leonardopicchiami / molecular_synthesis_and_reconstruction
Deep Learning And Applied Artificial Intelligence Project 2019/2020 - Molecular Synthesis & Reconstruction
molecular-generation synthesis reconstruction machine-learning deep-learning deep-generative-model molecules vae vae-pytorch pytorch python colab molecule-generation
Language:Jupyter Notebook 12
peterbjorgensen / msgnet
Tensorflow implementation of message passing neural networks for molecules and materials
machine-learning materials-science molecules tensorflow graphs
Language:Python 12
FinalCif
dkratzert / FinalCif
A CIF file finalizer for small molecule crystallography with as much automation as possible.
iucr cif shelxl bruker rigaku stoe crystallography structure report checkcif molecules
Language:Python 11
lukasturcani / moldoc
Make better chemistry documentation.
cheminformatics chemistry documentation molecules sphinx-extension visualization
Language:Python 11