ReleaseDeep Reinforcement Learning for de-novo Drug Design
Dgl LifesciPython package for graph neural networks in chemistry and biology
OddtOpen Drug Discovery Toolkit
GninaA deep learning framework for molecular docking
PubchempyPython wrapper for the PubChem PUG REST API.
Kekule.jsA Javascript cheminformatics toolkit.
IndigoUniversal cheminformatics libraries, utilities and database search tools
Ase aniANI-1 neural net potential with python interface (ASE)
Mol2vecMol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
StkA Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
ChemfilesLibrary for reading and writing chemistry files
Smiles TransformerOriginal implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.
Lstm chemImplementation of the paper - Generative Recurrent Networks for De Novo Drug Design.
MolvsMolecule Validation and Standardization
RdkitThe official sources for the RDKit library
CirpyPython wrapper for the NCI Chemical Identifier Resolver (CIR)
ScipipeRobust, flexible and resource-efficient pipelines using Go and the commandline
OpenbabelOpen Babel is a chemical toolbox designed to speak the many languages of chemical data.
TdcTherapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics
CdkThe Chemistry Development Kit
ThermoThermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
moleculeschemical graph theory library for JavaScript
Version3-1Version 2020 (3.1) of Chem4Word - A Chemistry Add-In for Microsoft Word
RcpiMolecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
AMPLThe 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
molmlA library to interface molecules and machine learning.
siriusSIRIUS 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)
protwisProtwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).
kGCNA graph-based deep learning framework for life science
PDNThe official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)
ScopyAn integrated negative design python library for desirable HTS/VS database design
pysmilesA lightweight python-only library for reading and writing SMILES strings
GLaDOSWeb Interface for ChEMBL @ EMBL-EBI
global-chemA Chemical Knowledge Graph of What is Common in the World.
e3fp3D molecular fingerprints
q2-qemistreeHierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
PADMEThis is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.
DrugExDeep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology
Version3Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word
molecular-VAEImplementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules
Jupyter DockJupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
chembienceA Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
senpaiMolecular dynamics simulation software