Projects in Awesome Lists tagged with molecules

https://github.com/biopandas/biopandas

Working with molecular structures in pandas DataFrames

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 16 May 2025

https://github.com/BioPandas/biopandas

Working with molecular structures in pandas DataFrames

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 18 Jul 2025

https://rasbt.github.io/biopandas

Working with molecular structures in pandas DataFrames

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 05 Sep 2025

https://github.com/HannesStark/EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

drug-discovery equivariance geometry graph-neural-networks molecules protein-structure proteins

Last synced: 03 Apr 2025

https://github.com/datamol-io/datamol

Molecular Processing Made Easy.

cheminformatics drug-design drug-discovery medicinal-chemistry molecule molecules python rdkit

Last synced: 08 Apr 2025

https://github.com/dewberryants/asciiMol

Curses based ASCII molecule viewer for terminals.

ascii cheminformatics chemistry molecules visualization

Last synced: 09 Jul 2025

https://github.com/jparkhill/tensormol

Tensorflow + Molecules = TensorMol

chemistry force-field machine-learning meta-dynamics molecular-dynamics molecular-simulation molecules monte-carlo neural-network simulation tensorflow

Last synced: 05 Apr 2025

https://github.com/jparkhill/TensorMol

Tensorflow + Molecules = TensorMol

chemistry force-field machine-learning meta-dynamics molecular-dynamics molecular-simulation molecules monte-carlo neural-network simulation tensorflow

Last synced: 04 May 2025

https://github.com/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 attention-mechanisms deep-learning equivariance molecules protein-folding transformers

Last synced: 15 May 2025

https://github.com/gcorso/torsional-diffusion

Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)

chemistry conformer-generator equivariance geometry machine-learning molecules neurips-2022 torsion-angles

Last synced: 07 Apr 2025

https://github.com/vijaydwivedi75/gnn-lspe

Source code for GNN-LSPE (Graph Neural Networks with Learnable Structural and Positional Representations), ICLR 2022

attention geometric-deep-learning gnn gnn-lspe graph-deep-learning graph-neural-networks graph-representation-learning graph-transformer graphs lspe message-passing molecules positional-encoding representation-learning transformer-networks transformers

Last synced: 03 Apr 2025

https://github.com/fzliu/radient

Radient turns many data types (not just text) into vectors for similarity search, clustering, regression analysis, and more.

audio embeddings etl fraud-detection graphs image-search images milvus molecular-search molecules recommender-system retrieval-augmented-generation semantic-search similarity-search text unstructured-data-etl vector-database vectors

Last synced: 06 Apr 2025

https://github.com/hannesstark/3dinfomax

Making self-supervised learning work on molecules by using their 3D geometry to pre-train GNNs. Implemented in DGL and Pytorch Geometric.

3d dgl-graph gnn graph graph-neural-networks graph-representation-learning molecules pytorch-geometric self-supervised-learning

Last synced: 07 Mar 2026

https://github.com/senya-ashukha/simple-equivariant-gnn

A short and easy PyTorch implementation of E(n) Equivariant Graph Neural Networks

deep-learning deep-neural-networks egnn equivariance gnn graph-neural-networks homo molecules neural-networks pytorch qm9

Last synced: 14 May 2025

https://github.com/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

Last synced: 09 May 2025

https://github.com/aimat-lab/gcnn_keras

Graph convolutions in Keras with TensorFlow, PyTorch or Jax.

graph-algorithms graph-convolution graph-networks graphs machine-learning molecules networks neural-networks ragged-tensors

Last synced: 03 Feb 2026

https://github.com/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

Last synced: 29 Oct 2025

https://github.com/samirelanduk/atomium

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

biology chemistry molecules proteins structural-biology

Last synced: 09 Apr 2025

https://github.com/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 molecules transformers

Last synced: 10 Aug 2025

https://github.com/benedekrozemberczki/pdn

The official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)

bert cheminformatics data-science deep-learning deepwalk gcn gnn gpt-3 graph-classification graph-neural-network graph2vec message-passing molecules multiplex network-science neural-message-passing node-classification pathfinder pytorch transformer

Last synced: 11 Apr 2025

https://github.com/atomind-ai/mlip-arena

Fair and transparent benchmark of machine-learned interatomic potentials (MLIPs), beyond basic error metrics

benchmark-framework interatomic-potentials machine-learning materials molecules quantum-chemistry

Last synced: 02 Apr 2026

https://github.com/arpitnarechania/d3-molecule

D3 based interactive visualization library + tool to make render atoms and molecules learning chemical bonding in a fun way.

atoms-in-molecules chemical-bonding chemoinformatics d3 interactive-visualizations javascript molecules open-source

Last synced: 27 Oct 2025

https://github.com/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

apisauce architecture atoms es6 eslint javascript molecules react react-native react-native-boilerplate react-native-starter react-native-template redux redux-saga reduxsauce saga scenes

Last synced: 13 Apr 2025

https://github.com/lukasturcani/stk-vis

A cross-platform application for visualization of molecular databases.

cheminformatics chemistry data-visualization database molecular-modeling molecular-structures molecules mongodb visualization

Last synced: 03 Mar 2026

https://github.com/avrabyt/st-speckmol

Streamlit Component for creating Speck molecular structures within Streamlit Web app.

bioinformatics molecules pdb python streamlit streamlit-component visualization

Last synced: 23 Apr 2026

https://github.com/alexriss/chemfilesviewer.jl

Julia library to visualize molecules and other chemical structures

3d chemistry julia julialang molecules render science visualization

Last synced: 07 May 2025

https://github.com/openchemistry/molecules

Common molecule fragments for visualization in Avogadro

chemistry common-molecule-fragments molecules

Last synced: 28 Feb 2026

https://github.com/andrewtarzia/mol-ellipsize

Molecular size calculation based on ellipsoid fitting over N conformers

chemistry high-throughput molecular-size molecules rdkit

Last synced: 03 Mar 2026

https://github.com/aacgn/atomic

A JavaScript library for building atomic interfaces with vertical and horizontal micro-frontends

angular atomic-template atoms dom-events javascript micro-frontend micro-frontends molecules postmessage reactjs single-spa transition-page virtual-dom vuejs

Last synced: 31 Aug 2025

https://github.com/devslem/mol-air

Molecular Reinforcement Learning with Adaptive Intrinsic Reward for Goal-directed Molecular Generation.

chemistry deep-reinforcement-learning drug-discovery molecular-modeling molecular-structure molecules reinforcement-learning

Last synced: 07 May 2025

https://github.com/lukasturcani/moldoc

Make better chemistry documentation!

cheminformatics chemistry documentation molecules sphinx-extension visualization

Last synced: 16 Mar 2025

https://github.com/jerboaburrow/simplefastopenatomicvisualiser

Visualise atomic and molecular system structures and trajectories

atoms ffmpeg lua molecular-dynamics molecules opengl visualisation

Last synced: 10 Jul 2025

https://github.com/dkratzert/finalcif

A CIF file finalizer for small molecule crystallography with as much automation as possible.

bruker checkcif cif crystallography iucr molecules report rigaku shelxl stoe structure

Last synced: 20 Mar 2025

https://github.com/openchemistry/fragments

Molecular fragments and inorganic ligands for rapidly building structures

chemistry common-molecule-fragments molecules openchemistry

Last synced: 25 Apr 2025

https://github.com/duboviy/pymolecule

:atom: Molecular viewer [Work in progress]

atom atoms-in-molecules molecular-graphics molecular-structures molecule molecules openbabel pybel pyglet

Last synced: 07 Sep 2025

https://github.com/radi0sus/xyzoverlay

Python 3 script for overlaying or superimposing two or more molecules. The overlayed / superimposed molecules can be displayed and the modified coordinates can be saved as xyz files. Coloring by atom or molecule is possible.

computational-chemistry coordinates coordination-chemistry dft inorganic-chemistry kabsch kabsch-algorithm molecule molecule-viewer molecule-visualization molecules overlay superposition xyz-files xyz-reader

Last synced: 19 Jul 2025

https://github.com/jaypalm/jsme-vue

Vue component wrapper around JSME-Editor

chemistry molecules

Last synced: 23 Oct 2025

https://github.com/lmmentel/panthera

Python package for computing thermochemical properties of molecules and solids in the anharmonic approximation.

anharmonicity chemistry enthalpy entropy molecules python solid-state-chemistry thermochemistry vibrations

Last synced: 12 May 2025

https://github.com/indyfree/moleculevr

VIS Molecule VR Project in Unreal Engine

molecules unrealengine virtual-reality vr

Last synced: 19 Apr 2025

https://github.com/radi0sus/xyzalign

Align atomic coordinates in xyz files. Align one or more atoms to x-, y- and z-axes. Set origin to a selected atom or a centroid of selected atoms. Rotate atomic coordinates about arbitrary angles. Translate atomic coordinates.

3d-coordinate align computational-chemistry coordinates coordination-chemistry dft inorganic-chemistry molecule molecules orca orca-quantum-chemistry orientation rotate rotation rotation-matrix translate translation xyz xyz-files xyz-reader

Last synced: 15 Oct 2025

https://github.com/ghutchis/conformer-scoring

Data and scripts relevant to an evaluation of force field methods for conformer scoring

chemistry conformer-scoring dft force-fields molecules pm7

Last synced: 25 Jul 2025

https://github.com/lszeremeta/molstruct

Convert chemical molecule data CSV files to structured data formats

bioschemas cheminformatics chemoinformatics csv docker-image json-ld microdata molecularentity molecule molecule-data molecules rdfa schema schema-org schemaorg

Last synced: 13 Apr 2025

https://github.com/isopropylcyanide/interaction-graph

Creating and analyzing interaction graphs based on boolean functions

boolean-function bruteforce cancer-research computation-graph cyclic-redundancy-check graph graph-algorithms java makefile molecules python research-project

Last synced: 03 Jun 2026

https://github.com/lszeremeta/megen

Molecular Entity Generator: Convenient online form to generate structured data about molecules

bioschemas docker docker-image generator json-ld microdata molecularentitly molecules php php-application rdfa schemaorg

Last synced: 11 May 2026

https://github.com/louffee/canada-design-system

Canada is the Louffee's Design System intended to make beautiful UIs with a lot of UX touches 🧭

accessibility atoms canada components design design-system molecules monorepo react storybook ui ux ux-ui

Last synced: 04 Oct 2025

https://github.com/thennen/counting-molecules

Automates counting and categorization of molecules in scanning probe microscopy images

cluster-analysis computer-vision image-analysis microscopy molecules zernike-moments

Last synced: 25 Jan 2026

https://github.com/dleidert/gnome-chemistry-utils

The Gnome Chemistry Utils provide some programs and library containing GTK widgets and some C++ classes related to chemistry. This is a migrated clone of the project's subversion repository. Upstream is not active anymore, but the program is still widely used. So please feel free to grab these sources and continue the project.

chemistry chemistry-formulas molecules

Last synced: 01 Aug 2025