Projects in Awesome Lists tagged with cheminformatics

https://github.com/rdkit/rdkit

The official sources for the RDKit library

c-plus-plus cheminformatics python rdkit

Last synced: 30 Jan 2026

https://github.com/openbabel/openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

c-plus-plus chemical-data chemical-toolbox cheminformatics chemistry

Last synced: 29 Apr 2025

https://github.com/lightaime/deep_gcns_torch

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

3d-point-clouds bioinformatics cheminformatics computer-vision data-mining deep-gcns deep-learning geometric-deep-learning graph-convolutional-networks graph-neural-networks pytorch science-research social-network

Last synced: 16 May 2025

https://github.com/scipipe/scipipe

Robust, flexible and resource-efficient pipelines using Go and the commandline

bioinformatics bioinformatics-pipeline cheminformatics dataflow fbp go golang pipeline scientific-workflows scipipe workflow workflow-engine

Last synced: 11 Apr 2026

https://github.com/mims-harvard/TDC

Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science

artificial-intelligence benchmarks bioinformatics biology biomedicine biotech cheminformatics chemistry datasets deep-learning drug-discovery machine-learning medicine precision-medicine therapeutics

Last synced: 30 Mar 2025

https://github.com/awslabs/dgl-lifesci

Python package for graph neural networks in chemistry and biology

bioinformatics cheminformatics deep-learning dgl drug-discovery geometric-deep-learning graph-neural-networks molecule

Last synced: 15 May 2025

https://github.com/calebbell/thermo

Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)

chemical-engineering cheminformatics chemistry combustion density environmental-engineering equation-of-state heat-capacity mechanical-engineering molecule physics process-simulation solubility surface-tension thermal-conductivity thermodynamics vapor-pressure viscosity

Last synced: 14 May 2025

https://github.com/molecularai/reinvent4

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

ai astrazeneca cheminformatics chemistry deep-learning denovo-design drug-design drug-discovery generative-ai ml molecule-generation neural-networks reinforcement-learning transfer-learning

Last synced: 16 Jan 2026

https://github.com/CalebBell/thermo

Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)

chemical-engineering cheminformatics chemistry combustion density environmental-engineering equation-of-state heat-capacity mechanical-engineering molecule physics process-simulation solubility surface-tension thermal-conductivity thermodynamics vapor-pressure viscosity

Last synced: 07 May 2025

https://github.com/cdk/cdk

The Chemistry Development Kit

bioinformatics blueobelisk cheminformatics chemistry code4lib java

Last synced: 21 Oct 2025

https://github.com/MolecularAI/aizynthfinder

A tool for retrosynthetic planning

astrazeneca chemical-reactions cheminformatics monte-carlo-tree-search neural-networks reaction-informatics

Last synced: 15 Mar 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/chemosim-lab/ProLIF

Interaction Fingerprints for protein-ligand complexes and more

cheminformatics docking drug-design drug-discovery mdanalysis molecular-dynamics rdkit

Last synced: 20 Nov 2025

https://github.com/mcs07/pubchempy

Python wrapper for the PubChem PUG REST API.

cheminformatics chemistry pubchem python

Last synced: 15 May 2025

https://github.com/chembl/chembl_webresource_client

Official Python client for accessing ChEMBL API

chembl cheminformatics chemistry chemoinformatics python rest rest-client

Last synced: 21 Oct 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/epam/Indigo

Universal cheminformatics toolkit, utilities and database search tools

bingo cheminformatics chemistry dotnet drug-discovery inchi indigo java molecule-visualization molfile postgresql python smarts smiles webassembly

Last synced: 16 Nov 2025

https://github.com/mcs07/PubChemPy

Python wrapper for the PubChem PUG REST API.

cheminformatics chemistry pubchem python

Last synced: 07 Apr 2025

https://github.com/isayev/ReLeaSE

Deep Reinforcement Learning for de-novo Drug Design

cheminformatics deeplearning drug-discovery molecular-modeling qsar reinforcement-learning

Last synced: 01 May 2025

https://github.com/epam/indigo

Universal cheminformatics toolkit, utilities and database search tools

bingo cheminformatics chemistry dotnet drug-discovery inchi indigo java molecule-visualization molfile postgresql python smarts smiles webassembly

Last synced: 19 Feb 2026

https://github.com/MolecularAI/Reinvent

astrazeneca cheminformatics denovo-design neural-networks reinforcement-learning transfer-learning

Last synced: 09 May 2025

https://github.com/experimental-design/bofire

Experimental design and (multi-objective) bayesian optimization.

active-learning bayesian-optimization cheminformatics experimental-design multiobjective-optimization

Last synced: 08 Apr 2025

https://github.com/partridgejiang/kekule.js

A Javascript cheminformatics toolkit.

cheminformatics chemistry javascript molecule

Last synced: 16 May 2025

https://github.com/AngelRuizMoreno/Jupyter_Dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

autodock autodock-vina cheminformatics computational-biology drug-design drug-discovery drug-repurposing jupyter-notebook ledock mdanalysis molecular-docking openbabel protein protein-structure py3dmol rdkit

Last synced: 22 Jul 2025

https://github.com/lukasturcani/stk

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

cheminformatics chemistry computational-chemistry computational-science materials-design materials-discoveries materials-science materials-screening molecular-evolution molecular-modeling molecular-structures reactions

Last synced: 04 Apr 2025

https://github.com/Mishima-syk/py4chemoinformatics

Python for chemoinformatics

cheminformatics chemoinformatics jupyter python rdkit scikit-learn

Last synced: 28 Mar 2025

https://github.com/MolecularAI/REINVENT4

AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.

ai astrazeneca cheminformatics chemistry deep-learning denovo-design drug-design drug-discovery generative-ai ml molecule-generation neural-networks reinforcement-learning transfer-learning

Last synced: 09 May 2025

https://github.com/isayev/ASE_ANI

ANI-1 neural net potential with python interface (ASE)

cheminformatics chemistry deep-learning force-field neural-network schrodinger-equation

Last synced: 04 May 2025

https://github.com/pierrehirel/atomsk

Atomsk: A Tool For Manipulating And Converting Atomic Data Files -

ab-initio atomeye atomic-design atomistic-simulations cheminformatics cif crystal-builder dislocation file-conversion gulp lammps materials-science open-source ovito physics-simulation polycrystal quantum-espresso science siesta vasp

Last synced: 16 May 2025

https://github.com/mojaie/moleculargraph.jl

Graph-based molecule modeling toolkit for cheminformatics

cheminformatics chemistry graph julia julia-language mcs molecular-modeling molecule toolkit

Last synced: 16 May 2025

https://github.com/mojaie/MolecularGraph.jl

Graph-based molecule modeling toolkit for cheminformatics

cheminformatics chemistry graph julia julia-language mcs molecular-modeling molecule toolkit

Last synced: 27 Mar 2025

https://github.com/cbouy/mols2grid

Interactive molecule viewer for 2D structures

cheminformatics jupyter molecule-viewer python rdkit visualization

Last synced: 05 Apr 2025

https://github.com/XuhanLiu/DrugEx

Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology

cheminformatics deep-learning graph-transformer multi-objective-optimization reinforcement-learning

Last synced: 11 Oct 2025

https://github.com/rdkit/rdkit-js

A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit .

cheminformatics drug-discovery javascript molecule molecule-viewer molecule-visualization node-js npm rdkit react wasm

Last synced: 15 May 2025

https://github.com/mcs07/molvs

Molecule Validation and Standardization

cheminformatics chemistry python rdkit standardization validation

Last synced: 06 Apr 2025

https://github.com/Global-Chem/global-chem

A Knowledge Graph of Common Chemical Names to their Molecular Definition

cheminformatics chemoinformatics graph-algorithms iupac organic-chemistry python scientific-visualization smiles visualization

Last synced: 17 Apr 2025

https://github.com/MolecularAI/ReinventCommunity

astrazeneca cheminformatics denovo-design jupyter-notebook neural-networks reinforcement-learning transfer-learning

Last synced: 09 May 2025

https://github.com/pckroon/pysmiles

A lightweight python-only library for reading and writing SMILES strings

cheminformatics hacktoberfest python smiles smiles-strings writing-smiles

Last synced: 08 Apr 2025

https://github.com/mcsorkun/chemplot

A python package for chemical space visualization.

chemical-space cheminformatics data-visualization dimensionality-reduction

Last synced: 21 Feb 2026

https://github.com/kuelumbus/rdkit-pypi

⚛️ RDKit Python Wheels on PyPI. 💻 pip install rdkit

cheminformatics pypi pypi-package python python-library rdkit

Last synced: 02 Mar 2026

https://github.com/chembl/FPSim2

Simple package for fast molecular similarity searches

cheminformatics chemistry gpu python similarity-search

Last synced: 09 May 2025

https://github.com/keiserlab/e3fp

3D molecular fingerprints

3d cheminformatics e3fp fingerprint molecular python

Last synced: 16 May 2025

https://github.com/sirius-ms/sirius

SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)

bioinformatics cheminformatics csi-fingerid denovo fingerid fragmentation-trees isotope-pattern java mass-spectra mass-spectrometry metabolomics molecular-formulas molecular-structures ms-data ms-spectra science sirius structure-elucidation

Last synced: 18 Feb 2026

https://github.com/mcs07/cirpy

Python wrapper for the NCI Chemical Identifier Resolver (CIR)

cheminformatics chemistry python

Last synced: 07 Apr 2025

https://github.com/cddleiden/drugex

De Novo Drug Design with RNNs and Transformers

cheminformatics de-novo-drug-design deep-learning drug-discovery reinforcement-learning

Last synced: 03 Nov 2025

https://github.com/topazape/lstm_chem

Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.

cheminformatics chemoinformatics denovo keras lstm machine-learning python3 rnn tensorflow2

Last synced: 13 Apr 2025

https://github.com/bgruening/galaxytools

:microscope::books: Galaxy Tool wrappers

cheminformatics galaxy galaxyproj hacktoberfest rna tools wrapper

Last synced: 16 Feb 2026

https://github.com/mcsorkun/ChemPlot

A python package for chemical space visualization.

chemical-space cheminformatics data-visualization dimensionality-reduction

Last synced: 30 Apr 2025

https://github.com/jvalegre/aqme

Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io

automation cheminformatics jupyter-notebooks python quantum-chemistry reproducibility workflows

Last synced: 13 Apr 2025

https://github.com/schrodinger/gpusimilarity

A Cuda/Thrust implementation of fingerprint similarity searching

cheminformatics chemistry gpu similarity-analysis

Last synced: 04 Mar 2026

https://github.com/ml-jku/clamp

Code for the paper Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language

assay-modeling cheminformatics contrastive-learning drug-discovery machine-learning qsar zero-shot

Last synced: 20 Jun 2025

https://github.com/acylation/obsidian-chem

Chemistry support for Obsidian. Rendering SMILES strings into chemistry structures.

cheminformatics chemistry obsidian obsidian-community obsidian-md obsidian-plugin

Last synced: 12 Sep 2025

https://github.com/Acylation/obsidian-chem

Chemistry support for Obsidian. Rendering SMILES strings into chemistry structures.

cheminformatics chemistry obsidian obsidian-community obsidian-md obsidian-plugin

Last synced: 10 Apr 2025

https://github.com/asarigun/awesome-denovo-papers

Awesome De novo drugs design papers

cheminformatics deep-generative-models deep-learning denovo-design diffusion-model drug-design drug-discovery gans gcn generative-model gnns machine-learning neural-networks paper target-based-drug variational-autoencoder

Last synced: 16 Jan 2026

https://github.com/mcocdawc/chemcoord

A python module for manipulating cartesian and internal coordinates.

chemical cheminformatics chemistry physics physics-simulation python python-library theoretical-spectroscopy

Last synced: 19 Jun 2025

https://github.com/chiang-yuan/llamp

A web app and Python API for multi-modal RAG framework to ground LLMs on high-fidelity materials informatics. An agentic materials scientist powered by @materialsproject, @langchain-ai, and @openai

ai4science cheminformatics language-model materials-informatics retrieval-augmented-generation

Last synced: 07 Apr 2025

https://github.com/ashvardanian/usearch-molecules

Searching for structural similarities across billions of molecules in milliseconds

aws-s3 bioinformatics biology cheminformatics chemistry compchem drug-discovery open-data opendata vector-search vector-search-engine

Last synced: 22 Mar 2025

https://github.com/aksub99/molecular-vae

Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"

cheminformatics chemistry deep-learning drug-discovery jupyter-notebook machine-learning materials-informatics materials-science molecular-structures natural-language-processing python pytorch variational-autoencoder

Last synced: 18 Mar 2025

https://github.com/crcollins/molml

A library to interface molecules and machine learning.

cheminformatics chemistry deep-learning machine-learning numpy python python-library quantum

Last synced: 19 Feb 2026

https://github.com/gmum/geo-gcn

The official implementation of the SGCN architecture.

cheminformatics convolutional-neural-networks graph-convolutional-networks missing-data

Last synced: 23 Oct 2025

https://github.com/cthoyt/chembl-downloader

Write reproducible code for getting and processing ChEMBL

bioinformatics chembl cheminformatics chemogenomics chemometrics machine-learning pharmacology proteochemometrics python reproducible-research toxicology

Last synced: 17 Mar 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/akensert/molgraph

Graph neural networks for molecular machine learning. Implemented and compatible with TensorFlow and Keras.

bioinformatics cheminformatics computational-biology computational-chemistry deep-learning graph-neural-networks graphs keras machine-learning tensorflow

Last synced: 12 Jul 2025

https://github.com/chopralab/lemon

A framework for rapidly mining structural information from the Protein Data Bank

cheminformatics chemistry computational-chemistry data-mining machine-learning structural-biology

Last synced: 04 Apr 2026

https://github.com/chem4word/version3

Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word

addin cheminformatics chemistry microsoft-office microsoft-word molecule openxml openxml-sdk structure

Last synced: 08 Apr 2025

https://github.com/dylanwal/chemistry_drawer

Draw molecules with plotly!

chemical cheminformatics chemistry molecule plotly rdkit smiles structure

Last synced: 14 Feb 2026

https://github.com/asad/smsd

SMSD — exact substructure & MCS search for chemical graphs.

bron-kerbosch cdk cheminformatics chemistry graph-matching java maven-central mcs rascal rrsplit smarts smsd stereo-aware substructure substructure-search vf2 vf2pp

Last synced: 12 Apr 2026

https://github.com/dylanwal/chemdraw

Draw molecules with plotly!

chemical cheminformatics chemistry molecule plotly rdkit smiles structure

Last synced: 18 Jun 2025

https://github.com/topazape/molecular-vae

Implementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules

cheminformatics chemoinformatics denovo machine-learning python3 pytorch vae

Last synced: 20 Jul 2025

https://github.com/jvalegre/robert

Automated machine learning protocols that start from CSV databases of descriptors or SMILES and produce publication-quality results in Chemistry studies with only one command line.

automation cheminformatics machine-learning python reproducibility scikit-learn workflows

Last synced: 13 Apr 2025

https://github.com/glambard/smiles-x

Autonomous characterization of molecular compounds from small datasets without descriptors

cheminformatics deep-learning materials-informatics natural-language-processing

Last synced: 10 Jul 2025

https://github.com/simonfqy/PADME

This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.

cheminformatics convolutional-neural-networks deep-learning

Last synced: 11 May 2025

https://github.com/smoren/molecular-ts

Virtual chemistry simultaion. Particle automata. Visualization of the behavior of particles in 2D and 3D space. Artifical life research.

3d artifical-life canvas cellular-automaton cheminformatics molecular-dynamics molecular-simulation particle-automata

Last synced: 23 Oct 2025

https://github.com/nanxstats/rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery

bioconductor bioinformatics cheminformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

Last synced: 22 Aug 2025

https://github.com/by256/icsg3d

3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning (JCIM 2020)

cheminformatics computational-chemistry computational-physics crystallography deep-learning representation-learning

Last synced: 30 Dec 2025

https://github.com/pnnl/cactus

LLM Agent that leverages cheminformatics tools to provide informed responses.

cheminformatics chemistry foundation-models llm llm-agent nlp science

Last synced: 12 Apr 2025

https://github.com/volkamerlab/maxsmi

maxsmi: a guide to SMILES augmentation. Find the optimal SMILES augmentation for accurate molecular prediction.

cheminformatics data-augmentation deep-learning

Last synced: 19 Feb 2026

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/biocore/q2-qemistree

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

cheminformatics fragmentation-trees metabolomics microbiome phylogenetics

Last synced: 13 May 2025

https://github.com/lhm30/pidginv2

PIDGIN Version 2: Prediction IncluDinG INactivity: Version 2 (LEGACY VERSION)

cheminformatics chemoinformatics molecule pubchem random-forest target target-prediction target-predictions weight

Last synced: 23 Oct 2025

https://github.com/martin-sicho/genui

The backend services of the GenUI framework. The backend provides the REST API used for molecular generation, QSAR modelling and chemical space visualization.

chemical-space cheminformatics data-science molecular-generation qsar rest-api visualization webapp

Last synced: 19 Jan 2026

https://github.com/ishan-kumar2/molecular_vae_pytorch

PyTorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"

automatics cheminformatics pytorch qsar smiles

Last synced: 15 Apr 2025

https://github.com/futianfan/dst

(differentiable) gradient-based optimization on a chemical graph for de novo molecule design/optimization (ICLR 2022)

cheminformatics denovo-design drug-design drug-discovery graph-neural-networks molecule-gene

Last synced: 12 Oct 2025

https://github.com/mcs07/mongodb-chemistry

Ideas for chemical similarity searches in MongoDB.

cheminformatics chemistry mongodb python search similarity

Last synced: 13 Apr 2025

https://github.com/ksharindam/chemcanvas

User-friendly 2D chemical structure drawing tool

chemical-drawing chemical-reactions cheminformatics chemistry drawing new pyqt

Last synced: 04 Mar 2026

https://github.com/MolecularAI/route-distances

Tools and routines to calculate distances between synthesis routes and to cluster them.

astrazeneca cheminformatics clustering

Last synced: 28 Sep 2025

https://github.com/gmum/mldd23

The repository for the course "Machine Learning in Drug Design" taught at the Jagiellonian University in 2023. The page is hosted by the machine learning research group GMUM.

cheminformatics computer-aided-drug-design deep-learning drug-design drug-discovery machine-learning pharmacoinformatics

Last synced: 07 Feb 2026

https://github.com/ethanbass/chromconverter

Parsers for chromatography data in R (HPLC-DAD/UV, GC-FID, MS)

cheminformatics chromatography fair-data gc-fid hplc hplc-dad hplc-uv metabolomics metabolomics-data open-data open-science r r-package rstats

Last synced: 19 Aug 2025

https://github.com/openforcefield/cmiles

Generate canonical molecule identifiers for quantum chemistry database

cheminformatics database forcefield forcefield-parameterization quantum-chemistry

Last synced: 18 Feb 2026

https://github.com/chem4word/version3-2

Version 2022 (3.2) of Chem4Word - A Chemistry Add-In for Microsoft Word

addin cheminformatics chemistry csharp microsoft-office microsoft-word molecule openxml openxml-sdk structure

Last synced: 22 Apr 2025

https://github.com/aspuru-guzik-group/dionysus

For analysis of calibration, performance, and generalizability of probabilistic models on small molecular datasets. Paper on RSC Digital Discovery: https://pubs.rsc.org/en/content/articlehtml/2023/dd/d2dd00146b

biology calibration cheminformatics chemistry probabilistic-models

Last synced: 21 Jul 2025