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The Top 232 Cheminformatics Open Source Projects on Github

Categories > Science > Cheminformatics
Rdkit ⭐ 1,479
The official sources for the RDKit library
Scipipe ⭐ 890
Robust, flexible and resource-efficient pipelines using Go and the commandline
Deep_gcns_torch ⭐ 766
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
Openbabel ⭐ 577
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
Tdc ⭐ 521
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development
Dgl Lifesci ⭐ 359
Python package for graph neural networks in chemistry and biology
Awesome Cheminformatics ⭐ 346
A curated list of Cheminformatics libraries and software.
Thermo ⭐ 344
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
Cdk ⭐ 322
The Chemistry Development Kit
Gnina ⭐ 261
A deep learning framework for molecular docking
Release ⭐ 232
Deep Reinforcement Learning for de-novo Drug Design
Oddt ⭐ 231
Open Drug Discovery Toolkit
Chembl_webresource_client ⭐ 217
Official Python client for accessing ChEMBL API.
Aizynthfinder ⭐ 197
A tool for retrosynthetic planning
Pubchempy ⭐ 190
Python wrapper for the PubChem PUG REST API.
Kekule.js ⭐ 186
A Javascript cheminformatics toolkit.
Indigo ⭐ 177
Universal cheminformatics toolkit, utilities and database search tools
Py4chemoinformatics ⭐ 147
Python for chemoinformatics
Reinvent ⭐ 139
Stk ⭐ 138
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
Ase_ani ⭐ 126
ANI-1 neural net potential with python interface (ASE)
Chemfiles ⭐ 107
Library for reading and writing chemistry files
Datamol ⭐ 105
Molecular Manipulation Made Easy.
Jupyter_dock ⭐ 104
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.
Senpai ⭐ 104
Molecular dynamics simulation software
Mol2vec ⭐ 103
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
Moleculargraph.jl ⭐ 100
Graph-based molecule modeling toolkit for cheminformatics
Scaffoldgraph ⭐ 100
ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.
Galaxytools ⭐ 95
🔬📚 Galaxy Tool wrappers
Lstm_chem ⭐ 91
Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.
Atomsk ⭐ 90
Atomsk: A Tool For Manipulating And Converting Atomic Data Files -
Chemspipy ⭐ 85
Python wrapper for the ChemSpider API
Kgcn ⭐ 80
A graph-based deep learning framework for life science
Ampl ⭐ 79
The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.
Deepscreen ⭐ 69
DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images
Pysmiles ⭐ 64
A lightweight python-only library for reading and writing SMILES strings
Molecules ⭐ 64
chemical graph theory library for JavaScript
Smiles Transformer ⭐ 62
Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.
Reinventcommunity ⭐ 60
Molvs ⭐ 55
Molecule Validation and Standardization
Cirpy ⭐ 54
Python wrapper for the NCI Chemical Identifier Resolver (CIR)
Py4chemoinformatics ⭐ 53
Python for chemoinformatics
Gpusimilarity ⭐ 52
A Cuda/Thrust implementation of fingerprint similarity searching
Rdkit Pypi ⭐ 50
⚛️ RDKit python wheels on PyPi. 💻 pip install rdkit-pypi
E3fp ⭐ 48
3D molecular fingerprints
Ani1_dataset ⭐ 45
A data set of 20 million calculated off-equilibrium conformations for organic molecules
Chemcoord ⭐ 45
A python module for manipulating cartesian and internal coordinates.
Pdn ⭐ 40
The official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)
Version3 ⭐ 39
Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word
Psikit ⭐ 37
psi4+RDKit
Molml ⭐ 36
A library to interface molecules and machine learning.
Sirius Libs ⭐ 35
sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java
Arpeggio ⭐ 33
Calculation of interatomic interactions in molecular structures
Chembience ⭐ 30
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
Sirius ⭐ 24
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)
Lemon ⭐ 22
A framework for rapidly mining structural information from the Protein Data Bank
Geo Gcn ⭐ 22
The official implementation of the geo-GCN architecture.
Padme ⭐ 20
This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.
Protwis ⭐ 20
Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
Molecular Vae ⭐ 20
Implementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules
Homebrew Cheminformatics ⭐ 19
Cheminformatics formulae for the Homebrew package manager
Ncdk ⭐ 19
The Chemistry Development Kit ported to .NET
Rcpi ⭐ 19
Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
Q2 Qemistree ⭐ 19
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Molecular Vae ⭐ 19
Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"
Pidginv2 ⭐ 18
PIDGIN Version 2: Prediction IncluDinG INactivity: Version 2 (LEGACY VERSION)
Scopy ⭐ 18
An integrated negative design python library for desirable HTS/VS database design
Glados ⭐ 18
New Web Interface for ChEMBL @ EMBL-EBI
Cmiles ⭐ 17
Generate canonical molecule identifiers for quantum chemistry database
Stk Vis ⭐ 17
A cross-platform application for visualization of molecular databases.
Iupac_smiles_plus ⭐ 17
IUPAC SMILES+ Specification
Chemixnet ⭐ 16
Mixed DNN Architectures for Predicting Properties using Multiple Molecular Representations
Mongodb Chemistry ⭐ 16
Ideas for chemical similarity searches in MongoDB.
Pidginv3 ⭐ 15
Protein target prediction using random forests and reliability-density neighbourhood analysis
Gpcrdb_data ⭐ 15
This repository is the collection point of reference data for the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
Organic Chemistry Reaction Prediction Using Nmt ⭐ 13
organic chemistry reaction prediction using NMT with Attention
Version3 1 ⭐ 13
Version 3.1 of Chem4Word - A Chemistry Add-In for Microsoft Word
Rdkit Js ⭐ 12
The official JavaScript release of RDKit https://github.com/rdkit/rdkit .
Vespucci ⭐ 12
A free (open source), cross-platform tool for spectroscopic data analysis and imaging
Molpher Lib ⭐ 12
C++/Python Library for Systematic Chemical Space Exploration
Icsg3d ⭐ 11
Official implementation of "3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning" (JCIM) 2020
Aqml ⭐ 10
Amons-based quantum machine learning for quantum chemistry
Tangram ⭐ 10
🔲⚛️ A collection of molecular modelling tools for UCSF Chimera
Pysmash ⭐ 10
Smash molecule and obtain significant fragments
Smiles X ⭐ 10
Autonomous characterization of molecular compounds from small datasets without descriptors
Biodb ⭐ 10
An R package framework for accessing biological and chemical databases and developing or extending new connectors.
Moldoc ⭐ 9
Make better chemistry documentation.
Route Distances ⭐ 9
Tools and routines to calculate distances between synthesis routes and to cluster them.
E3fp Paper ⭐ 9
3D molecular fingerprints (E3FP) paper repo
Deep Purpose Tutorial ⭐ 9
Repository for the HackBio'2021 Internship for Team Drug-Development-A
Awesome Structural Bioinformatics ⭐ 8
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
Mofid ⭐ 8
A system for rapid identification and analysis of metal-organic frameworks
Graphdot ⭐ 8
Primary repo at https://gitlab.com/yhtang/graphdot
Rdkit Blog ⭐ 8
Maxsmi ⭐ 8
maxsmi: a guide to SMILES augmentation. Find the optimal SMILES augmentation for accurate molecular prediction.
Chemplot ⭐ 8
A python package for chemical space visualization.
Cdkbook ⭐ 8
Groovy Cheminformatics with the Chemistry Development Kit
Semanticchemistry ⭐ 7
Chemical Information Ontology
Sdfeater ⭐ 7
Always hungry SDF chemical file format parser with many output formats
Ocsr Project ⭐ 7
Optical Chemical Structure Recognition Tool (based on OSRA)
1-100 of 232 projects

Related Projects

Python Cheminformatics Projects (109)
Chemistry Cheminformatics Projects (88)
Python Chemistry Cheminformatics Projects (49)
Bioinformatics Cheminformatics Projects (37)
Jupyter Notebook Cheminformatics Projects (35)
Cheminformatics Drug Discovery Projects (34)
Cheminformatics Rdkit Projects (32)
Machine Learning Cheminformatics Projects (27)
Deep Learning Cheminformatics Projects (25)
Cheminformatics Chemoinformatics Projects (23)
Molecule Cheminformatics Projects (22)
Advertising 📦 9
All Projects
Application Programming Interfaces 📦 120
Applications 📦 181
Artificial Intelligence 📦 72
Blockchain 📦 70
Build Tools 📦 111
Cloud Computing 📦 79
Code Quality 📦 28
Collaboration 📦 30
Command Line Interface 📦 48
Community 📦 81
Companies 📦 60
Compilers 📦 60
Computer Science 📦 74
Configuration Management 📦 39
Content Management 📦 167
Control Flow 📦 197
Data Formats 📦 77
Data Processing 📦 266
Data Storage 📦 132
Economics 📦 60
Frameworks 📦 198
Games 📦 122
Graphics 📦 103
Hardware 📦 148
Integrated Development Environments 📦 47
Learning Resources 📦 147
Legal 📦 28
Libraries 📦 119
Lists Of Projects 📦 21
Machine Learning 📦 336
Mapping 📦 61
Marketing 📦 15
Mathematics 📦 55
Media 📦 228
Messaging 📦 97
Networking 📦 304
Operating Systems 📦 84
Operations 📦 120
Package Managers 📦 52
Programming Languages 📦 229
Runtime Environments 📦 96
Science 📦 42
Security 📦 375
Social Media 📦 26
Software Architecture 📦 70
Software Development 📦 68
Software Performance 📦 57
Software Quality 📦 127
Text Editors 📦 45
Text Processing 📦 131
User Interface 📦 310
User Interface Components 📦 465
Version Control 📦 29
Virtualization 📦 68
Web Browsers 📦 38
Web Servers 📦 25
Web User Interface 📦 194
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