96 Open Source Cheminformatics Software Projects
Free and open source cheminformatics code projects including engines, APIs, generators, and tools.
Openbabel 610 ⭐
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
Thermo 345 ⭐
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
Mol2vec 162 ⭐
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
Lukasturcani Stk 139 ⭐
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
Smiles Transformer 142 ⭐
Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.
Ani1_dataset 56 ⭐
A data set of 20 million calculated off-equilibrium conformations for organic molecules
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.
Deepscreen 74 ⭐
DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images
Chembience 33 ⭐
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
Sirius Libs 36 ⭐
sirius-libs - Metabolomics mass spectrometry framework for molecular formula identification of small molecules written in Java
Chopralab Lemon 41 ⭐
A framework for rapidly mining structural information from the Protein Data Bank
Padme 29 ⭐
This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.
Rcpi 21 ⭐
Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.
Pidginv3 30 ⭐
Protein target prediction using random forests and reliability-density neighbourhood analysis
Aksub99 Molecular Vae 25 ⭐
Pytorch implementation of the paper "Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules"
Smiles X 31 ⭐
Autonomous characterization of molecular compounds from small datasets without descriptors
Molecular Vae 28 ⭐
Implementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules
Organic Chemistry Reaction Prediction Using Nmt 24 ⭐
organic chemistry reaction prediction using NMT with Attention
Q2 Qemistree 20 ⭐
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Boecker Lab Sirius 23 ⭐
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)
Tangram 13 ⭐
:black_square_button::atom_symbol: A collection of molecular modelling tools for UCSF Chimera
Kotori & Scopy 23 ⭐
An integrated negative design python library for desirable HTS/VS database design
Chemixnet 16 ⭐
Mixed DNN Architectures for Predicting Properties using Multiple Molecular Representations
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).
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).
Deep_gcns_torch 840 ⭐
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
Mims Harvard Tdc 516 ⭐
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development
Jupyter_dock 114 ⭐
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.
Pdn 40 ⭐
The official PyTorch implementation of "Pathfinder Discovery Networks for Neural Message Passing" (WebConf '21)
Icsg3D 18 ⭐
Official implementation of "3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning" (JCIM 2020)
Biodb 10 ⭐
An R package framework for accessing biological and chemical databases and developing or extending new connectors.
Pubchemprops 11 ⭐
A convenient wrapper around PubChem PUG REST API that allows to search for many compound properties available at PubChem with ease
Genui 12 ⭐
The backend services of the GenUI framework. The backend provides the REST API used for molecular generation, QSAR modelling and chemical space visualization.
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.