Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists tagged with cheminformatics
A curated list of projects in awesome lists tagged with cheminformatics .
https://github.com/rdkit/rdkit
The official sources for the RDKit library
c-plus-plus cheminformatics python rdkit
Last synced: 30 Sep 2024
https://github.com/lightaime/deep_gcns_torch
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
3d-point-clouds bioinformatics cheminformatics computer-vision data-mining deep-gcns deep-learning geometric-deep-learning graph-convolutional-networks graph-neural-networks pytorch science-research social-network
Last synced: 30 Sep 2024
https://github.com/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
Last synced: 01 Oct 2024
https://github.com/openbabel/openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
c-plus-plus chemical-data chemical-toolbox cheminformatics chemistry
Last synced: 01 Oct 2024
https://github.com/mims-harvard/TDC
Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science
artificial-intelligence benchmarks bioinformatics biology biomedicine biotech cheminformatics chemistry datasets deep-learning drug-discovery machine-learning medicine precision-medicine therapeutics
Last synced: 01 Aug 2024
https://github.com/awslabs/dgl-lifesci
Python package for graph neural networks in chemistry and biology
bioinformatics cheminformatics deep-learning dgl drug-discovery geometric-deep-learning graph-neural-networks molecule
Last synced: 26 Sep 2024
https://github.com/calebbell/thermo
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
chemical-engineering cheminformatics chemistry combustion density environmental-engineering equation-of-state heat-capacity mechanical-engineering molecule physics process-simulation solubility surface-tension thermal-conductivity thermodynamics vapor-pressure viscosity
Last synced: 26 Sep 2024
https://github.com/CalebBell/thermo
Thermodynamics and Phase Equilibrium component of Chemical Engineering Design Library (ChEDL)
chemical-engineering cheminformatics chemistry combustion density environmental-engineering equation-of-state heat-capacity mechanical-engineering molecule physics process-simulation solubility surface-tension thermal-conductivity thermodynamics vapor-pressure viscosity
Last synced: 03 Aug 2024
https://github.com/MolecularAI/aizynthfinder
A tool for retrosynthetic planning
astrazeneca chemical-reactions cheminformatics monte-carlo-tree-search neural-networks reaction-informatics
Last synced: 30 Jul 2024
https://github.com/cdk/cdk
The Chemistry Development Kit
bioinformatics blueobelisk cheminformatics chemistry code4lib java
Last synced: 02 Aug 2024
https://github.com/datamol-io/datamol
Molecular Processing Made Easy.
cheminformatics drug-design drug-discovery medicinal-chemistry molecule molecules python rdkit
Last synced: 26 Sep 2024
https://github.com/chembl/chembl_webresource_client
Official Python client for accessing ChEMBL API
chembl cheminformatics chemistry chemoinformatics python rest rest-client
Last synced: 03 Aug 2024
https://github.com/mcs07/PubChemPy
Python wrapper for the PubChem PUG REST API.
cheminformatics chemistry pubchem python
Last synced: 01 Aug 2024
https://github.com/dewberryants/asciiMol
Curses based ASCII molecule viewer for terminals.
ascii cheminformatics chemistry molecules visualization
Last synced: 04 Aug 2024
https://github.com/isayev/ReLeaSE
Deep Reinforcement Learning for de-novo Drug Design
cheminformatics deeplearning drug-discovery molecular-modeling qsar reinforcement-learning
Last synced: 02 Aug 2024
https://github.com/epam/indigo
Universal cheminformatics toolkit, utilities and database search tools
bingo cheminformatics chemistry dotnet drug-discovery inchi indigo java molecule-visualization molfile postgresql python smarts smiles webassembly
Last synced: 28 Sep 2024
https://github.com/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.
autodock autodock-vina cheminformatics computational-biology drug-design drug-discovery drug-repurposing jupyter-notebook ledock mdanalysis molecular-docking openbabel protein protein-structure py3dmol rdkit
Last synced: 09 Aug 2024
https://github.com/partridgejiang/kekule.js
A Javascript cheminformatics toolkit.
cheminformatics chemistry javascript molecule
Last synced: 26 Sep 2024
https://github.com/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.
cheminformatics chemistry computational-chemistry computational-science materials-design materials-discoveries materials-science materials-screening molecular-evolution molecular-modeling molecular-structures reactions
Last synced: 05 Aug 2024
https://github.com/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
Last synced: 03 Aug 2024
https://github.com/isayev/ASE_ANI
ANI-1 neural net potential with python interface (ASE)
cheminformatics chemistry deep-learning force-field neural-network schrodinger-equation
Last synced: 02 Aug 2024
https://github.com/Mishima-syk/py4chemoinformatics
Python for chemoinformatics
cheminformatics chemoinformatics jupyter python rdkit scikit-learn
Last synced: 31 Jul 2024
https://github.com/weisscharlesj/scicompforchemists
Scientific Computing for Chemists text for teaching basic computing skills to chemistry students using Python, Jupyter notebooks, and the SciPy stack. This text makes use of a variety of packages including NumPy, SciPy, matplotlib, pandas, seaborn, NMRglue, SymPy, scikit-image, and scikit-learn.
biochemistry bioinformatics book chemical cheminformatics chemistry chemists computer-programming computing jupyter-lab jupyter-notebooks jupyterlab nmr numpy python science scientific-computing scipy simulations textbook
Last synced: 30 Sep 2024
https://github.com/weisscharlesj/SciCompforChemists
Scientific Computing for Chemists text for teaching basic computing skills to chemistry students using Python, Jupyter notebooks, and the SciPy stack. This text makes use of a variety of packages including NumPy, SciPy, matplotlib, pandas, seaborn, NMRglue, SymPy, scikit-image, and scikit-learn.
biochemistry bioinformatics book chemical cheminformatics chemistry chemists computer-programming computing jupyter-lab jupyter-notebooks jupyterlab nmr numpy python science scientific-computing scipy simulations textbook
Last synced: 09 Aug 2024
https://github.com/pierrehirel/atomsk
Atomsk: A Tool For Manipulating And Converting Atomic Data Files -
ab-initio atomeye atomic-design atomistic-simulations cheminformatics cif crystal-builder dislocation file-conversion gulp lammps materials-science open-source ovito physics-simulation polycrystal quantum-espresso science siesta vasp
Last synced: 28 Sep 2024
https://github.com/mojaie/moleculargraph.jl
Graph-based molecule modeling toolkit for cheminformatics
cheminformatics chemistry graph julia julia-language mcs molecular-modeling molecule toolkit
Last synced: 26 Sep 2024
https://github.com/mojaie/MolecularGraph.jl
Graph-based molecule modeling toolkit for cheminformatics
cheminformatics chemistry graph julia julia-language mcs molecular-modeling molecule toolkit
Last synced: 31 Jul 2024
https://github.com/XuhanLiu/DrugEx
Deep learning toolkit for Drug Design with Pareto-based Multi-Objective optimization in Polypharmacology
cheminformatics deep-learning graph-transformer multi-objective-optimization reinforcement-learning
Last synced: 01 Oct 2024
https://github.com/Global-Chem/global-chem
A Knowledge Graph of Common Chemical Names to their Molecular Definition
cheminformatics chemoinformatics graph-algorithms iupac organic-chemistry python scientific-visualization smiles visualization
Last synced: 01 Aug 2024
https://github.com/pckroon/pysmiles
A lightweight python-only library for reading and writing SMILES strings
cheminformatics hacktoberfest python smiles smiles-strings writing-smiles
Last synced: 01 Oct 2024
https://github.com/rdkit/rdkit-js
A powerful cheminformatics and molecule rendering toolbelt for JavaScript, powered by RDKit .
cheminformatics drug-discovery javascript molecule molecule-viewer molecule-visualization node-js npm rdkit react wasm
Last synced: 26 Sep 2024
https://github.com/keiserlab/e3fp
3D molecular fingerprints
3d cheminformatics e3fp fingerprint molecular python
Last synced: 26 Sep 2024
https://github.com/chembl/FPSim2
Simple package for fast molecular similarity searches
cheminformatics chemistry gpu python similarity-search
Last synced: 03 Aug 2024
https://github.com/mcsorkun/ChemPlot
A python package for chemical space visualization.
chemical-space cheminformatics data-visualization dimensionality-reduction
Last synced: 02 Aug 2024
https://github.com/schrodinger/gpusimilarity
A Cuda/Thrust implementation of fingerprint similarity searching
cheminformatics chemistry gpu similarity-analysis
Last synced: 03 Aug 2024
https://github.com/jvalegre/aqme
Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io
automation cheminformatics jupyter-notebooks python quantum-chemistry reproducibility workflows
Last synced: 03 Aug 2024
https://github.com/Acylation/obsidian-chem
Chemistry support for Obsidian. Rendering SMILES strings into chemistry structures.
cheminformatics chemistry obsidian obsidian-community obsidian-md obsidian-plugin
Last synced: 01 Aug 2024
https://github.com/chem4word/version3
Version 3 of Chem4Word - A Chemistry Add-In for Microsoft Word
addin cheminformatics chemistry microsoft-office microsoft-word molecule openxml openxml-sdk structure
Last synced: 26 Sep 2024
https://github.com/chiang-yuan/llamp
A web app and Python API for multi-modal RAG framework to ground LLMs on high-fidelity materials informatics. An agentic materials scientist powered by @materialsproject, @langchain-ai, and @openai
ai4science cheminformatics language-model materials-informatics retrieval-augmented-generation
Last synced: 02 Aug 2024
https://github.com/simonfqy/PADME
This is the repository containing the source code for my Master's thesis research, about predicting drug-target interaction using deep learning.
cheminformatics convolutional-neural-networks deep-learning
Last synced: 03 Aug 2024
https://github.com/dylanwal/chemistry_drawer
Draw molecules with plotly!
chemical cheminformatics chemistry molecule plotly rdkit smiles structure
Last synced: 26 Sep 2024
https://github.com/by256/icsg3d
3-D Inorganic Crystal Structure Generation and Property Prediction via Representation Learning (JCIM 2020)
cheminformatics computational-chemistry computational-physics crystallography deep-learning representation-learning
Last synced: 02 Aug 2024
https://github.com/lhm30/pidginv2
PIDGIN Version 2: Prediction IncluDinG INactivity: Version 2 (LEGACY VERSION)
cheminformatics chemoinformatics molecule pubchem random-forest target target-prediction target-predictions weight
Last synced: 26 Sep 2024
https://github.com/mawansui/pubchemprops
A convenient wrapper around PubChem PUG REST API that allows to search for many compound properties available at PubChem with ease
cheminformatics chemistry chemoinformatics pubchem python python3
Last synced: 01 Oct 2024
https://github.com/chemistry/chemical-libraries
Common Chemical Libraries
cheminformatics chemistry monorepo periodic-table
Last synced: 28 Sep 2024
https://github.com/streamlit/streamlit-ketcher
Chemical molecule custom component for Streamlit apps
cheminformatics chemistry editor molecule
Last synced: 26 Sep 2024
https://github.com/rohanv01/molecule_format_converter
This jupyter notebook let's you convert sdf to pdb or SMILES to pdbqt file formats for a batch of compounds to perform cheminformatics and drug discovery projects
cheminformatics drug-design drug-discovery molecule problem-solving smiles
Last synced: 26 Sep 2024
https://github.com/iktos/molecule-representation
Interactif molecule represnetations as react components
cheminformatics chemistry molecule-viewer react typescript
Last synced: 26 Sep 2024
https://github.com/cbouy/bokehmol
Bokeh extensions to plot molecules easily
bokeh cheminformatics interactive-visualizations jupyter rdkit
Last synced: 28 Sep 2024
https://github.com/thomasjewson/molecular3dlengthdescriptors
A 3D conformational based molecular descriptor set for use in QSPR and Machine Learning.
3d cheminformatics chemistry conformer crystallography descriptor learning machine molecule rdkit
Last synced: 26 Sep 2024
https://greglandrum.github.io/rdkit-blog/
RDKit blog
cheminformatics computational-chemistry rdkit
Last synced: 03 Aug 2024
https://github.com/ardcore/fit_transform
Calculate and apply the optimal transformation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.
cheminformatics kabsch molecular-modeling rmsd
Last synced: 27 Sep 2024
https://github.com/andy-wilkinson/chemmltoolkit
A set of useful Python functionality for machine learning in chemistry
cheminformatics chemistry machine-learning tensorflow
Last synced: 29 Sep 2024
https://github.com/labimotion/labimotion.github.io
LabIMotion Schema provides a contract for the Template used and details the properties, types, and other constraints that the Template should have.
cheminformatics chemistry chemotion json-schema labimotion
Last synced: 30 Sep 2024
https://github.com/maxischuh/twinbooster
Package for TwinBooster. Enables fast and powerful zero-shot molecular property prediction.
cheminformatics chemistry large-language-models machine-learning molecular-property-prediction molecule
Last synced: 26 Sep 2024
https://github.com/seatonullberg/chemfiles-cli
A simple chemistry file conversion CLI which wraps the chemfiles library
cheminformatics chemistry cli computational-chemistry file-converter
Last synced: 02 Oct 2024
https://github.com/quantori/structure-seer
The implementation, training and evaluation of a Structure Seer machine learning model designed for reconstruction of adjacency of a molecular graph from the labelling of its nodes.
cheminformatics graph graph-convolutional-network machine-learning ml molecular-graph molecular-graph-learning molecule molecule-generation nmr-data nmr-spectroscopy
Last synced: 26 Sep 2024
https://github.com/seatonullberg/materials-embedding-book
An interactive guide to using hidden layer embeddings as descriptors of materials
cheminformatics computational-chemistry crystallography materials-informatics materials-science
Last synced: 02 Oct 2024