cheminformatics

There are 56 repositories under cheminformatics topic.

rdkit / rdkit
The official sources for the RDKit library
c-plus-plus cheminformatics python rdkit
Language:HTML 2408
lightaime / deep_gcns_torch
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
graph-neural-networks geometric-deep-learning 3d-point-clouds deep-gcns data-mining pytorch computer-vision bioinformatics cheminformatics social-network science-research deep-learning graph-convolutional-networks
Language:Python 1120
scipipe / scipipe
Robust, flexible and resource-efficient pipelines using Go and the commandline
bioinformatics bioinformatics-pipeline cheminformatics dataflow fbp go golang pipeline scientific-workflows scipipe workflow workflow-engine
Language:Go 1054
openbabel / openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
chemistry chemical-data cheminformatics c-plus-plus chemical-toolbox
Language:C++ 982
mims-harvard / TDC
Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science
machine-learning therapeutics drug-discovery datasets biology chemistry biomedicine bioinformatics cheminformatics deep-learning benchmarks artificial-intelligence precision-medicine medicine
Language:Jupyter Notebook 924
awslabs / dgl-lifesci
Python package for graph neural networks in chemistry and biology
deep-learning graph-neural-networks dgl cheminformatics bioinformatics geometric-deep-learning drug-discovery molecule
Language:Python 680
hsiaoyi0504 / awesome-cheminformatics
A curated list of Cheminformatics libraries and software.
awesome awesome-list cheminformatics bioinformatics chemistry
636
CalebBell / thermo
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
thermodynamics chemistry cheminformatics chemical-engineering mechanical-engineering viscosity density heat-capacity thermal-conductivity surface-tension combustion environmental-engineering solubility vapor-pressure equation-of-state molecule process-simulation physics
Language:Python 585
gnina / gnina
A deep learning framework for molecular docking
convolutional-neural-networks cheminformatics computational-chemistry molecular-modeling drug-discovery
Language:C++ 550
MolecularAI / aizynthfinder
A tool for retrosynthetic planning
astrazeneca chemical-reactions cheminformatics monte-carlo-tree-search neural-networks reaction-informatics
Language:Python 526
cdk / cdk
The Chemistry Development Kit
code4lib chemistry java cheminformatics bioinformatics blueobelisk
Language:Java 466
datamol-io / datamol
Molecular Processing Made Easy.
python molecule rdkit drug-discovery drug-design molecules cheminformatics medicinal-chemistry
Language:Python 422
oddt / oddt
Open Drug Discovery Toolkit
scoring docking screening python rdkit openbabel cheminformatics
Language:Python 393
mcs07 / PubChemPy
Python wrapper for the PubChem PUG REST API.
python cheminformatics pubchem chemistry
Language:Python 356
dewberryants / asciiMol
Curses based ASCII molecule viewer for terminals.
chemistry cheminformatics molecules visualization ascii
Language:Python 349
chembl / chembl_webresource_client
Official Python client for accessing ChEMBL API
python rest-client rest chemistry cheminformatics chemoinformatics chembl
Language:Python 347
isayev / ReLeaSE
Deep Reinforcement Learning for de-novo Drug Design
deeplearning reinforcement-learning cheminformatics molecular-modeling drug-discovery qsar
Language:Jupyter Notebook 341
MolecularAI / Reinvent
cheminformatics neural-networks astrazeneca reinforcement-learning denovo-design transfer-learning
Language:Python 332
chemosim-lab / ProLIF
Interaction Fingerprints for protein-ligand complexes and more
molecular-dynamics rdkit drug-design docking cheminformatics mdanalysis
Language:Python 320
DSPsleeporg / smiles-transformer
Original implementation of the paper "SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery" by Shion Honda et al.
deep-learning cheminformatics python transformer chemistry pytorch
Language:Jupyter Notebook 282
epam / Indigo
Universal cheminformatics toolkit, utilities and database search tools
indigo bingo cheminformatics chemistry python dotnet microsoft-sql-server postgresql webassembly java oracle molfile smiles inchi smarts
Language:C++ 277
AngelRuizMoreno / 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.
molecular-docking autodock autodock-vina ledock mdanalysis rdkit openbabel cheminformatics computational-biology jupyter-notebook py3dmol protein protein-structure drug-discovery drug-repurposing drug-design
Language:Jupyter Notebook 243
partridgejiang / Kekule.js
A Javascript cheminformatics toolkit.
cheminformatics molecule chemistry javascript
Language:JavaScript 243
samoturk / mol2vec
Mol2vec - an unsupervised machine learning approach to learn vector representations of molecular substructures
python machine-learning cheminformatics
Language:Python 242
stk
lukasturcani / stk
A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
chemistry cheminformatics reactions computational-science computational-chemistry materials-science materials-design materials-discoveries materials-screening molecular-structures molecular-modeling molecular-evolution
Language:Python 234
wjm41 / molplotly
add-on to plotly which show molecule images on mouseover!
plotly-dash data-visualization rdkit cheminformatics molecule-viewer
Language:Python 228
isayev / ASE_ANI
ANI-1 neural net potential with python interface (ASE)
neural-network deep-learning chemistry cheminformatics schrodinger-equation force-field
Language:Python 217
Mishima-syk / py4chemoinformatics
Python for chemoinformatics
cheminformatics chemoinformatics jupyter python rdkit scikit-learn
Language:Jupyter Notebook 217
MolecularAI / REINVENT4
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
ai astrazeneca cheminformatics chemistry deep-learning denovo-design drug-design drug-discovery generative-ai ml molecule-generation neural-networks reinforcement-learning transfer-learning
Language:Python 205
cbouy / mols2grid
Interactive molecule viewer for 2D structures
rdkit molecule-viewer visualization python jupyter cheminformatics
Language:Python 204
XuhanLiu / DrugEx
Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology
deep-learning multi-objective-optimization graph-transformer reinforcement-learning cheminformatics
Language:Python 184
mojaie / MolecularGraph.jl
Graph-based molecule modeling toolkit for cheminformatics
cheminformatics molecular-modeling chemistry toolkit julia julia-language molecule mcs graph
Language:Julia 183
pierrehirel / atomsk
Atomsk: A Tool For Manipulating And Converting Atomic Data Files -
science atomic-design ab-initio file-conversion atomistic-simulations dislocation materials-science cheminformatics polycrystal vasp quantum-espresso lammps gulp cif atomeye ovito siesta crystal-builder open-source physics-simulation
Language:Fortran 181
benb111 / awesome-small-molecule-ml
A curated list of resources for machine learning for small-molecule drug discovery
awesome-list machine-learning cheminformatics drug-discovery awesome bioinformatics
170
chemfiles / chemfiles
Library for reading and writing chemistry files
computational-chemistry library files compchem cheminformatics chemistry hacktoberfest
Language:C++ 159
ScaffoldGraph
UCLCheminformatics / ScaffoldGraph
ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.
rdkit networkx scaffold-networks scaffold-trees cheminformatics murcko fragments molecules scaffolds hiers chemistry computational-chemistry
Language:Python 159