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Top 57 cheminformatics open source projects

Awesome Cheminformatics
A curated list of Cheminformatics libraries and software.
Release
Deep Reinforcement Learning for de-novo Drug Design
Dgl Lifesci
Python package for graph neural networks in chemistry and biology
Oddt
Open Drug Discovery Toolkit
Gnina
A deep learning framework for molecular docking
Pubchempy
Python wrapper for the PubChem PUG REST API.
Chembl webresource client
Official Python client for accessing ChEMBL API.
Kekule.js
A Javascript cheminformatics toolkit.
Indigo
Universal cheminformatics libraries, utilities and database search tools
Ase ani
ANI-1 neural net potential with python interface (ASE)
Mol2vec
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
Aizynthfinder
A tool for retrosynthetic planning
Stk
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
Chemfiles
Library for reading and writing chemistry files
Smiles Transformer
Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.
Lstm chem
Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.
Molvs
Molecule Validation and Standardization
Rdkit
The official sources for the RDKit library
Cirpy
Python wrapper for the NCI Chemical Identifier Resolver (CIR)
Scipipe
Robust, flexible and resource-efficient pipelines using Go and the commandline
Openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
Tdc
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics
Cdk
The Chemistry Development Kit
Thermo
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
Rcpi
Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
awesome-small-molecule-ml
A curated list of resources for machine learning for small-molecule drug discovery
AMPL
The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.
rdkit-pypi
⚛️ RDKit Python Wheels on PyPi. 💻 pip install rdkit-pypi
molml
A library to interface molecules and machine learning.
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)
protwis
Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
Scopy
An integrated negative design python library for desirable HTS/VS database design
pysmiles
A lightweight python-only library for reading and writing SMILES strings
mongodb-chemistry
Ideas for chemical similarity searches in MongoDB.
q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
PADME
This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.
DrugEx
Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology
homebrew-cheminformatics
Cheminformatics formulae for the Homebrew package manager
molecular-VAE
Implementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules
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.
chembience
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
1-57 of 57 cheminformatics projects