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The Top 349 Cheminformatics Open Source Projects

Categories > Science > Cheminformatics
Rdkit ⭐ 1,855
The official sources for the RDKit library
dependent packages 20total releases 42most recent commit 5 hours ago
Deep_gcns_torch ⭐ 940
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
most recent commit 4 months ago
Scipipe ⭐ 911
Robust, flexible and resource-efficient pipelines using Go and the commandline
total releases 47most recent commit 8 months ago
Openbabel ⭐ 740
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
dependent packages 5total releases 2most recent commit 4 days ago
Awesome Python Chemistry ⭐ 733
A curated list of Python packages related to chemistry
most recent commit a month ago
Tdc ⭐ 724
Therapeutics Data Commons: Artificial Intelligence Foundation for Therapeutic Science
dependent packages 1total releases 26most recent commit 3 days agopypi PyTDC} Downloads
Dgl Lifesci ⭐ 509
Python package for graph neural networks in chemistry and biology
dependent packages 1total releases 15most recent commit 4 days agopypi dgllife} Downloads
Awesome Cheminformatics ⭐ 456
A curated list of Cheminformatics libraries and software.
most recent commit 2 days ago
Thermo ⭐ 408
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
dependent packages 10total releases 55most recent commit 2 months agopypi thermo} Downloads
Teachopencadd ⭐ 398
TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
total releases 5most recent commit a month ago
Cdk ⭐ 386
The Chemistry Development Kit
dependent packages 6total releases 16most recent commit a day ago
Gnina ⭐ 354
A deep learning framework for molecular docking
most recent commit a month ago
Aizynthfinder ⭐ 321
A tool for retrosynthetic planning
most recent commit 6 days ago
Asciimol ⭐ 312
Curses based ASCII molecule viewer for linux terminals.
total releases 9most recent commit 6 months ago
Datamol ⭐ 273
Molecular Manipulation Made Easy.
dependent packages 1total releases 44most recent commit 5 days agopypi datamol} Downloads
Chembl_webresource_client ⭐ 252
Official Python client for accessing ChEMBL API.
most recent commit 7 months ago
Avogadrio ⭐ 248
Worship your favorite molecule by setting it as your wallpaper.
most recent commit a year ago
Oddt ⭐ 241
Open Drug Discovery Toolkit
total releases 26most recent commit 10 months ago
Release ⭐ 232
Deep Reinforcement Learning for de-novo Drug Design
most recent commit a year ago
Reinvent ⭐ 223
most recent commit 4 months ago
Indigo ⭐ 217
Universal cheminformatics toolkit, utilities and database search tools
dependent packages 3total releases 13most recent commit 2 days agopypi epam.indigo} Downloads
Kekule.js ⭐ 215
A Javascript cheminformatics toolkit.
most recent commit 16 days ago
Pubchempy ⭐ 190
Python wrapper for the PubChem PUG REST API.
dependent packages 13total releases 5most recent commit a year agopypi PubChemPy} Downloads
Stk ⭐ 174
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
dependent packages 2total releases 104most recent commit 18 days agopypi stk} Downloads
Smiles Transformer ⭐ 154
Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.
most recent commit 9 months ago
Py4chemoinformatics ⭐ 147
Python for chemoinformatics
most recent commit a year ago
Moleculargraph.jl ⭐ 146
Graph-based molecule modeling toolkit for cheminformatics
most recent commit 2 months ago
Molplotly ⭐ 142
add-on to plotly which show molecule images on mouseover!
total releases 10most recent commit 9 days ago
Jupyter_dock ⭐ 134
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.
most recent commit 6 months ago
Mols2grid ⭐ 133
Interactive molecule viewer for 2D structures
total releases 12most recent commit 3 months ago
Ase_ani ⭐ 126
ANI-1 neural net potential with python interface (ASE)
most recent commit 2 years ago
Chemfiles ⭐ 120
Library for reading and writing chemistry files
dependent packages 2total releases 4most recent commit 2 months ago
Atomsk ⭐ 117
Atomsk: A Tool For Manipulating And Converting Atomic Data Files -
total releases 4most recent commit 20 days ago
Senpai ⭐ 117
Molecular dynamics simulation software
most recent commit 5 months ago
Drugex ⭐ 115
Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology
most recent commit 4 months ago
Cheminformatics ⭐ 114
Facilitates searching, screening, and organizing large chemical databases
most recent commit 3 months ago
Galaxytools ⭐ 106
🔬📚 Galaxy Tool wrappers
most recent commit 2 days ago
Scaffoldgraph ⭐ 105
ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.
total releases 8most recent commit 10 months ago
Pysmiles ⭐ 103
A lightweight python-only library for reading and writing SMILES strings
dependent packages 1total releases 2most recent commit 2 days agopypi pysmiles} Downloads
Mol2vec ⭐ 103
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
most recent commit 3 years ago
Ampl ⭐ 101
The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.
most recent commit 19 days ago
Global Chem ⭐ 100
A General Public Dictionary of Common Chemical Names to SMILES
total releases 135most recent commit 5 days ago
Rdkit Pypi ⭐ 94
⚛️ RDKit Python Wheels on PyPi. 💻 pip install rdkit
dependent packages 66total releases 32most recent commit 6 days agopypi rdkit-pypi} Downloads
Kgcn ⭐ 93
A graph-based deep learning framework for life science
most recent commit 5 months ago
Lstm_chem ⭐ 91
Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.
most recent commit a year ago
Awesome_bigdata_ai_drugdiscovery ⭐ 89
A collection of resources useful for leveraging big data and AI for drug discovery. It mainly serves as an orientation for new lab folks. It may be biased towards my lab interest.
most recent commit a year ago
Deepscreen ⭐ 85
DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images
most recent commit a year ago
Chemspipy ⭐ 85
Python wrapper for the ChemSpider API
total releases 7most recent commit 4 years ago
Deepsmiles ⭐ 81
DeepSMILES - A variant of SMILES for use in machine-learning
total releases 2most recent commit 2 years ago
E3fp ⭐ 81
3D molecular fingerprints
dependent packages 1total releases 7most recent commit 6 months agopypi e3fp} Downloads
Reinventcommunity ⭐ 75
most recent commit 7 months ago
Opensourcemolecularmodeling.github.io ⭐ 72
Catalog of Open Source Molecular Modeling Projects
most recent commit 2 months ago
Ani1_dataset ⭐ 71
A data set of 20 million calculated off-equilibrium conformations for organic molecules
total releases 3most recent commit 4 months ago
Fpsim2 ⭐ 67
Simple package for fast molecular similarity searches
total releases 6most recent commit 3 days ago
Molecules ⭐ 64
chemical graph theory library for JavaScript
most recent commit 6 years ago
Rdkit Js ⭐ 60
A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit .
total releases 51most recent commit 4 days ago
Awesome Small Molecule Ml ⭐ 59
A curated list of resources for machine learning for small-molecule drug discovery
most recent commit 6 months ago
Opencadd ⭐ 57
A Python library for structural cheminformatics
total releases 7most recent commit 3 months ago
Molvs ⭐ 55
Molecule Validation and Standardization
total releases 10most recent commit 3 years ago
Cirpy ⭐ 54
Python wrapper for the NCI Chemical Identifier Resolver (CIR)
dependent packages 3total releases 2most recent commit 6 years agopypi CIRpy} Downloads
Py4chemoinformatics ⭐ 53
Python for chemoinformatics
most recent commit 2 years ago
Openchemlib ⭐ 53
Open source Java-based chemistry library
total releases 167most recent commit 2 days ago
Gpusimilarity ⭐ 52
A Cuda/Thrust implementation of fingerprint similarity searching
most recent commit a year ago
Chemplot ⭐ 50
A python package for chemical space visualization.
total releases 9most recent commit 2 months ago
Auto Qchem ⭐ 50
Auto-QChem is an automated workflow for the generation and storage of DFT calculations for organic molecules.
most recent commit 25 days ago
Version3 ⭐ 48
Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word
most recent commit 5 months ago
Chemcoord ⭐ 46
A python module for manipulating cartesian and internal coordinates.
total releases 8most recent commit 9 months ago
Sirius ⭐ 45
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)
most recent commit 5 days ago
Pdn ⭐ 44
The official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)
most recent commit 4 months ago
Chemkit ⭐ 44
A C++ library for molecular modelling, cheminformatics and molecular visualization.
most recent commit 3 years ago
Indigo ⭐ 42
Indigo: a cheminformatics toolkit. Bingo: RDBMS data cartridge for Oracle, MS SQL Server, and PostgreSQL
most recent commit a year ago
Psikit ⭐ 37
psi4+RDKit
total releases 6most recent commit 2 years ago
Retrosynthesis_planner ⭐ 36
Retrosynthesis planner
most recent commit 2 years ago
Aqme ⭐ 36
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
most recent commit a day ago
Molml ⭐ 36
A library to interface molecules and machine learning.
total releases 12most recent commit 3 years ago
Sirius Libs ⭐ 35
sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java
most recent commit 2 years ago
Geo Gcn ⭐ 35
The official implementation of the SGCN architecture.
most recent commit 10 months ago
Workshop ⭐ 35
most recent commit 2 years ago
Inchlib.js ⭐ 33
InCHlib (Interactive Cluster Heatmap library)
most recent commit 2 years ago
Arpeggio ⭐ 33
Calculation of interatomic interactions in molecular structures
most recent commit 2 years ago
Dbparser ⭐ 33
Source code for the R package, "dbparser" (i.e. DrugBank Parser)
total releases 9most recent commit 2 years ago
Chembl Downloader ⭐ 33
Write reproducible code for getting and processing ChEMBL
most recent commit 4 days ago
Chembience ⭐ 33
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
most recent commit 9 months ago
Scikit Chem ⭐ 32
A high level cheminformatics package for the Scientific Python stack, built on RDKit.
total releases 5most recent commit 3 years ago
Visualizer ⭐ 31
most recent commit 2 months ago
Awesome Deep Learning 4 Life Sciences ⭐ 29
A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).
most recent commit 2 days ago
Chemcore ⭐ 28
A cheminformatics toolkit for Rust.
total releases 8most recent commit a year ago
Cdkbook ⭐ 28
Groovy Cheminformatics with the Chemistry Development Kit
most recent commit a month ago
Protwis ⭐ 25
Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
most recent commit 4 days ago
Chemalot ⭐ 25
chemalot: a command-line cheminformatics open-source package
most recent commit 5 months ago
Rcpi ⭐ 24
Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
most recent commit 5 months ago
Web_molkit ⭐ 24
Web Molecular Toolkit: cheminformatics functionality in TypeScript
most recent commit 4 days ago
Docker Recipes ⭐ 23
🐳 Dockerfiles to build Galaxy images
most recent commit 4 years ago
Stk Vis ⭐ 23
A cross-platform application for visualization of molecular databases.
most recent commit 9 months ago
Lemon ⭐ 22
A framework for rapidly mining structural information from the Protein Data Bank
total releases 5most recent commit 3 years ago
Mx ⭐ 21
Essential Cheminformatics
most recent commit 13 years ago
Maxsmi ⭐ 21
maxsmi: a guide to SMILES augmentation. Find the optimal SMILES augmentation for accurate molecular prediction.
total releases 2most recent commit a month ago
Icsg3d ⭐ 20
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning (JCIM 2020)
most recent commit a month ago
Padme ⭐ 20
This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.
most recent commit 3 years ago
Ncdk ⭐ 19
The Chemistry Development Kit ported to .NET
dependent packages 1total releases 20most recent commit 2 years agonuget NCDK} Downloads
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