chemoinformatics

There are 17 repositories under chemoinformatics topic.

ysig / GraKeL
A scikit-learn compatible library for graph kernels
graph-kernels graph-classification scikit-learn graph-mining bioinformatics chemoinformatics graph-similarity graph-similarity-algorithms
Language:Python 630
chembl / chembl_webresource_client
Official Python client for accessing ChEMBL API
python rest-client rest chemistry cheminformatics chemoinformatics chembl
Language:Python 425
weisscharlesj / SciCompforChemists
Scientific Computing for Chemists with Python is a free book for teaching basic coding skills to chemists using Python, Jupyter notebooks, and the other Python software. This textbook teaches a variety of Python packages including NumPy, SciPy, matplotlib, pandas, seaborn, nmrglue, SymPy, scikit-image, scikit-learn, and others.
chemists scipy numpy python jupyterlab jupyter-notebooks chemistry computing scientific-computing chemical simulations biochemistry textbook book computer-programming coding data-visualization nmr chemoinformatics
Language:Jupyter Notebook 295
Marsilea-viz / marsilea
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
heatmap visualization upset oncoprint x-layout data-visualization data-science matplotlib python bioinformatics chemoinformatics physics
Language:Python 293
scikit-fingerprints / scikit-fingerprints
Scikit-learn compatible library for molecular fingerprints and chemoinformatics
bioinformatics chemical-data chemical-toolbox cheminformatics chemistry chemoinformatics machine-learning python scikit-learn
Language:Python 277
ismorphism / DeepECG
ECG classification programs based on ML/DL methods
bioinformatics cardio chemoinformatics cinc-challenge convolutional-neural-networks dataset deep-learning ecg ecg-classification electrode-voltage-measurements heart-rate keras mit-bh neural-network physiological-signals physiology python qrs recurrent-neural-networks tensorflow
Language:Python 270
DrrDom / crem
CReM: chemically reasonable mutations framework
chemical-space chemoinformatics
Language:Jupyter Notebook 249
Mishima-syk / py4chemoinformatics
Python for chemoinformatics
chemoinformatics scikit-learn cheminformatics python rdkit jupyter
Language:Jupyter Notebook 230
Global-Chem / global-chem
A Knowledge Graph of Common Chemical Names to their Molecular Definition
python cheminformatics chemoinformatics organic-chemistry graph-algorithms iupac scientific-visualization smiles visualization
Language:Jupyter Notebook 170
DeepMol
BioSystemsUM / DeepMol
DeepMol: A Machine and Deep Learning Framework for Computational Chemistry
chemoinformatics deep-learning machine-learning
Language:Python 160
jajupmochi / graphkit-learn
A python package for graph kernels, graph edit distances, and graph pre-image problem.
graph-kernels walks paths kernel-methods graph-representations pattern-recognition machine-learning chemoinformatics pre-image graph-edit-distance
Language:Jupyter Notebook 128
MolecularAI / DockStream
DockStream: A Docking Wrapper to Enhance De Novo Molecular Design
astrazeneca chemoinformatics denovo-design jupyter-notebook molecular-docking reinforcement-learning
Language:Python 125
topazape / LSTM_Chem
Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.
chemoinformatics cheminformatics keras python3 machine-learning lstm rnn denovo tensorflow2
Language:Jupyter Notebook 118
joofio / py4chemoinformatics
Python for chemoinformatics
chemoinformatics cheminformatics python rdkit jupyter scikit-learn deep-learning chemistry drug-discovery drug-design cv machine-learning
Language:Jupyter Notebook 113
DrrDom / pmapper
3D pharmacophore signatures and fingerprints
chemoinformatics pharmacophore
Language:Python 108
OSU-NLP-Group / ScienceAgentBench
[ICLR'25] ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
ai4science code-generation language-agent large-language-models task-automation bioinformatics chemoinformatics cognitive-neuroscience geoscience
Language:Python 107
Mishima-syk / psikit
psi4+RDKit
cheminformatics chemistry chemoinformatics psi quantum-chemistry rdkit
Language:Python 104
molinfo-vienna / CDPKit
The Chemical Data Processing Toolkit
chemoinformatics
Language:C++ 102
zotko / xyz2graph
Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
molecular-graph chemistry molecule chemoinformatics xyz-files xyz-reader atomic-coordinates plotly 3d-plot networkx molecule-visualization chemical-structures computational-chemistry data-visualization molecular-modeling scientific-computing
Language:Python 86
BALL-Project / ball
The Biochemical Algorithms Library
c-plus-plus structural-biology chemoinformatics force-field computational-biology drug-design
Language:C++ 73
xieguigang / mzkit
Data toolkits for processing NMR, MALDI MSI, MALDI single cell, Raman Spectroscopy, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.
visualbasic metadna lc-ms gc-ms kegg metabolomics r-sharp ms-imaging gcxgc maldi chemoinformatics single-cell single-cell-metabolism mass-spectrometry mzkit raman-spectroscopy ms-dial lipidomics
Language:Visual Basic .NET 64
PaccMann / chemical_representation_learning_for_toxicity_prediction
Chemical representation learning paper in Digital Discovery
deep-learning toxicity-prediction qsar chemoinformatics property-prediction pytorch
Language:Jupyter Notebook 63
DrugBud-Suite / CADD_Vault
chemistry cheminformatics chemoinformatics computational-chemistry computational-biology computational-physics compchem drug-discovery drugs drug-repurposing drug-design protein-ligand-interactions virtual-screening molecular-dynamics molecular-modeling molecular-simulation sbvs
Language:HTML 59
chembl / GLaDOS
Web Interface for ChEMBL @ EMBL-EBI
chembl chemistry cheminformatics chemoinformatics webapp drug-targets drug-discovery molecular-structures
Language:JavaScript 53
ManzoorElahi / organic-chemistry-reaction-prediction-using-NMT
organic chemistry reaction prediction using NMT with Attention
attention-mechanism cheminformatics chemistry chemoinformatics keras machine-learning nlp
Language:Python 51
topazape / molecular-VAE
Implementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules
chemoinformatics cheminformatics pytorch python3 machine-learning vae denovo
Language:Python 47
arpitnarechania / d3-molecule
D3 based interactive visualization library + tool to make render atoms and molecules learning chemical bonding in a fun way.
d3 chemoinformatics molecules atoms-in-molecules chemical-bonding javascript open-source interactive-visualizations
Language:HTML 46
chembience / chembience
A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.
docker django django-rest-framework rdkit docker-compose postgresql chemistry chemoinformatics python jupyter-notebook cheminformatics
Language:Python 46
qcscine / molassembler
Chemoinformatics toolkit with support for inorganic molecules
chemistry chemoinformatics conformer-generator data-structures graph-algorithms molecule molecule-builder stereochemistry
Language:C++ 43
linchemin
syngenta / linchemin
Linked Chemical Information. LinChemIn is a Python toolkit that leverages the native connectivity of Chemical Reaction Data and provides actionable insights. The toolkit provides a program interface to several Computer-Aided Synthesis Prediction tools, allowing users to devise and calculate metrics on predicted Chemical Synthetic Routes.
casp chemoinformatics python synthesis
Language:Python 43
lhm30 / PIDGINv3
Protein target prediction using random forests and reliability-density neighbourhood analysis
target-prediction cheminformatics chemoinformatics protein-ligand-interactions applicability-domain reliability-density rdkit
Language:Python 41
metgem / metgem
Calculation and visualization of molecular networks based on t-SNE algorithm
chemistry chemoinformatics mass-spectrometry cosine-similarity networking graph network metabolomics
Language:Python 35
ci-lab-cz / pharmd
MD pharmacophores and virtual screening
chemoinformatics pharmacophore-models
Language:Python 33
Croydon-Brixton / pymol-remote
Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows)
bioinformatics chemoinformatics protein-design pymol-extension
Language:Python 33
Accio / AMIDD
Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)
drug-discovery applied-mathematics informatics teaching bioinformatics chemoinformatics computing statistics
Language:TeX 32
lhm30 / PIDGINv2
PIDGIN Version 2: Prediction IncluDinG INactivity: Version 2 (LEGACY VERSION)
target target-predictions target-prediction pubchem weight random-forest molecule cheminformatics chemoinformatics
Language:Python 31