GitHub topics: rdkit

Repositories

suneelbvs/MolEncoders

Python package for molecular representations and encodings

Language: Python - Size: 8.79 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

kubor/alpine-rdkit

RDKit on alpine with Anaconda

Language: Dockerfile - Size: 6.84 KB - Last synced at: 9 months ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 1

rvianello/docker-postgres-rdkit

The PostgreSQL image, just extended with the RDKit cartridge

Language: Dockerfile - Size: 16.6 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 12 - Forks: 6

lhm30/PIDGINv3

Protein target prediction using random forests and reliability-density neighbourhood analysis

Language: Python - Size: 5.27 MB - Last synced at: 25 days ago - Pushed at: almost 5 years ago - Stars: 40 - Forks: 14

gmattedi/chemicalspace

Object-oriented Representation for Chemical Spaces

Language: Jupyter Notebook - Size: 1.59 MB - Last synced at: 19 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

InformaticsMatters/squonk

Squonk platform and computational notebook

Language: Java - Size: 123 MB - Last synced at: 18 days ago - Pushed at: about 4 years ago - Stars: 8 - Forks: 3

DrReetuSharma/molecular_innovations-for-KPGT-Knowledge-guided-Pre-training-of-Graph-Transformer-

Knowledge-guided-Pre-training-of-Graph-Transformer: The primary aim of this project is to leverage knowledge-guided pre-training techniques for enhancing the performance of graph transformers in molecular property prediction and drug discovery.

Language: Python - Size: 591 KB - Last synced at: 2 months ago - Pushed at: 10 months ago - Stars: 2 - Forks: 0

EvitanRelta/reaction-geognn

Re-implementation of GeoGNN in PyTorch + DGL, and further adapted to predict reaction properties.

Language: Jupyter Notebook - Size: 36.1 MB - Last synced at: 26 days ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

kotori-y/pySmash

Smash molecule and obtain significant fragments

Language: Jupyter Notebook - Size: 12.5 MB - Last synced at: 18 days ago - Pushed at: almost 4 years ago - Stars: 17 - Forks: 3

alexandreklr/PGdet

A uni project developped to take an organic molecule written in SMILES and give back the point group

Language: Python - Size: 69.3 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 2

sustainable-processes/tljh-rxns

Plugin for TLJH for computational chemistry

Language: Python - Size: 2.93 KB - Last synced at: 11 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 1

DocMinus/psi4_rdkit

Quant Chem python scripts using PSI4 and RdKit

Language: Jupyter Notebook - Size: 308 KB - Last synced at: 11 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

moltinginstar/discovering-telomerase-inhibitors

Discovering telomerase inhibitors with machine learning.

Language: Jupyter Notebook - Size: 4.91 MB - Last synced at: 23 days ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

ritabratamaiti/Chem-Faiss

This projects utilises vector similarity search from Faiss, in conjunction with chemical fingerprinting to build a scalabale similarity search architecture for compounds/molecules.

Language: Jupyter Notebook - Size: 3.21 MB - Last synced at: 5 days ago - Pushed at: about 4 years ago - Stars: 19 - Forks: 3

Bobidan97/Cheminformatics

Cheminformatics based project that aims to assess the diversity of the known inhibitors of SarsCov-2 proteases taken from COVID Moonshot project.

Language: Python - Size: 2.86 MB - Last synced at: 12 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1

ciw-project-2023/coaler

CoAler = Core Aligner (Multi-Alignment of Molecules)

Language: C++ - Size: 23.2 MB - Last synced at: 19 days ago - Pushed at: 12 months ago - Stars: 8 - Forks: 1

quantaosun/webdock

Open-Sourced. Easy docking in your browser without any login requirement. Post processing and interaction diagram included.

Language: Jupyter Notebook - Size: 6.62 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

caiyingchun/pychem

Various python script about cheminformatics.

Language: Jupyter Notebook - Size: 50.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 1

Aaryesh-AD/GU-Drug-Pro-Toolkit

A Comprehensive Tool for Drug Property and Likeness Prediction.

Language: Python - Size: 190 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

icanswim/qchem

An exploration of the state of the art in the application of data science to quantum chemistry.

Language: Jupyter Notebook - Size: 3.73 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 3

bio-grids/autodocking-utils

Docker implementation of autodocking, openbabel, rdkit and lots of molecular dynamics utilities.

Language: Dockerfile - Size: 6.66 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

vandan-revanur/pychemprojections

Visualize various molecule projections using Python 🎨

Language: Python - Size: 67.9 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 4 - Forks: 0

ChidhvilasTanay/drug_discovery_coronavirus_CHEMBL

A Drug Discovery method using CHEMBL database, Lipinski Parameters, molecular fingerprint (padel) for SARS coronavirus 3C-like proteinase.

Language: Jupyter Notebook - Size: 510 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

cheminfolab/flask

An electronic lab notebook based on react and django.

Language: TypeScript - Size: 1.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

AmyQ20/Tutorials

Random tutorials (RDKit, GPR)

Language: HTML - Size: 206 KB - Last synced at: about 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

chembience/chembience

A Docker-based, cloudable platform for the development of chemoinformatics-centric web applications and microservices.

Language: Python - Size: 4.17 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 44 - Forks: 3

greglandrum/rdkit-blog-fastpages

Language: Jupyter Notebook - Size: 31.5 MB - Last synced at: 17 days ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 7

vandan-revanur/pychemovality

Estimate ovality of molecules 🌐

Language: Fortran - Size: 56.3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 0

gulabpatel/Graph_Neural_Network

Language: Jupyter Notebook - Size: 14.4 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0

DocMinus/RxnTransformDescriptors

Python code for reaction transform descriptors (TDs)

Language: Python - Size: 33.2 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

TanushGoel/PharmaceuticAI

An iterative process that uses two machine learning models to generate the best inhibitors for a target protein to help reduce the time and cost of the drug discovery process

Language: Jupyter Notebook - Size: 8.94 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 2

Franky1/Streamlit-RDKit

Streamlit example project with RDKit

Language: Makefile - Size: 37.1 KB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

bmrb-io/smolscripts

small molecule processing scripts

Language: Python - Size: 552 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

rdkit-rs/rdkit-sys

Rust crate for linking against the RDKit C++ API

Size: 76.2 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 19 - Forks: 6

suneelbvs/rdkit_tutorials

rdKit basics (provided jupyter notebooks are custom curated and will help the users to start working on rdKit)

Language: Jupyter Notebook - Size: 1.4 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 22 - Forks: 5

silicos-it/spectrophores-boost

Spectrophore technology with part of it in C++/Boost

Size: 4.91 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 1 - Forks: 1

kcncell/Deepchem_toxicityPredictionModel

This is an introductory deep learning model which uses the Deepchem package. Lots of credit has to be given to the authors(Ramsundar B., Eastman P., Walters P., Pande V.) of the book "Deep Learning for the Life Sciences". This book has been a gold mine in terms of my exploration and journey in DeepLearning in the field of biochemistry.

Language: Jupyter Notebook - Size: 5.86 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

albags/ProjectTargetPredictionApp

Target Prediction and Similarity 2D&3D using Python scientific libraries

Language: HTML - Size: 8.11 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 1

mcsorkun/Conformer-Search

A simple workflow for minimum energy conformer search based on force field optimization methods (UFF and MMFF94) available from RDKit.

Language: Python - Size: 195 KB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 7 - Forks: 4

ThWIC-AutoQSPR/iterstruc

Language: Python - Size: 319 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

c-feldmann/lassohighlight

Tool to add substructure highlighting to molecules drawn with RDKit

Language: Python - Size: 706 KB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 1

c-feldmann/rdkit_heatmaps

A package to draw custom heatmaps on molecular depictions of RDKit

Language: Python - Size: 3.7 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 8 - Forks: 0

santuchal/molecule_descriptors_and_fingerprint

SMILE to Descriptors and Fingerprint Generators

Language: Python - Size: 16.6 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

kareemjeiroudi/molecules_and_ml

An online repository to access my bachelor project files wherever I go. However, this might be of interest to some bioinformaticians. For full description please refer to the README file.

Language: Jupyter Notebook - Size: 490 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 1

SylwiaNowakowska/Graph_Neural_Network_Drug_Discovery

Classification of molecules' ability to inhibit HIV with Graph Neural Networks (PyTorch Geometric) - work in progress.

Language: Jupyter Notebook - Size: 552 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

nbehrnd/RegioSQM Fork of jensengroup/RegioSQM

A quick prediction of selectivities for the electrophilic substitution of homo- & heteroaromatic systems (Kromann et al., 2018ChemSci660 (http://dx.doi.org/10.1039/C7SC04156J) now ported to Python3.

Language: Python - Size: 9.78 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

liskovaf/COCONUT

Feature interrelation profiling using COCONUT and ZINC database

Language: Jupyter Notebook - Size: 200 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

the-metabolic-disassembler/metadisassembler

Language: Jupyter Notebook - Size: 3.08 MB - Last synced at: 16 days ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

jeffrichardchemistry/pySiRC

Simple web application for prediction of reaction rate constant through machine learning models using molecular fingerprints.

Language: Python - Size: 233 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 11 - Forks: 4

rinikerlab/PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

Language: Python - Size: 218 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 15 - Forks: 13

farhad-abdi/InSilicoQ

Quantum Computing and Machine Learning for Drug Design and Proteins Engineering

Language: Python - Size: 487 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1

jcathalina/rdk-rs

Rust bindings for the C++ API of RDKit.

Language: Rust - Size: 50.8 KB - Last synced at: 1 day ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

yamasakih/docker-compose-razi

docker-compose + JupyterNotebook + RDKit database cartridge + PostgreSQL

Language: Jupyter Notebook - Size: 537 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 8 - Forks: 6

Niaev/teste-de-selecao_altox 📦

Teste de Seleção: Serviço Flask para Desenho Molecular

Language: Python - Size: 124 KB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

AI4PFAS/AI4PFAS

Dataset and code for "Uncertainty-Informed Deep Transfer Learning of PFAS Toxicity"

Language: Jupyter Notebook - Size: 1.24 GB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 10 - Forks: 0

joofio/py4chemoinformatics Fork of Mishima-syk/py4chemoinformatics

Python for chemoinformatics

Language: Jupyter Notebook - Size: 24.3 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 88 - Forks: 26

dualword/dualword-chem

chemical viewer

Language: C++ - Size: 306 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

dualword/Molsketch-Mod Fork of timvdm/Molsketch

Molsketch 2D molecular editor

Language: C++ - Size: 5.22 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

silicos-it/qed

The QED (Quantitative Estimation of Drug-likeness) molecular descriptor to use in combination with RDKit

Language: Python - Size: 135 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 6

kirkdotcam/rdkitexplore

Language: Jupyter Notebook - Size: 29.3 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 1

suneelbvs/Streamlit-app

Streamlit multipage app on rdKit Cheatsheet

Language: Python - Size: 8.79 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 0

Henrique-rt/QSAR_applicability_domain_convex_hull

Allows to visualize and analyze if the molecules of the test set and of an external set are contained in the convex hull defined by the molecules of the training set.

Language: Python - Size: 56.6 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 2

linc-ufpa-br/structure-analysis-BBB

Calculation of peptide molecular descriptors.

Language: Python - Size: 1.3 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

suneelbvs/ChemAxon_UGM2022

Do you want integrate Chemaxon knime nodes in Jupyter Notebook. This repo contains the knime workflows, and jupyter notebooks that used for demonstration during #ChemAxon #UGM2022

Language: Jupyter Notebook - Size: 69.3 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0

kuteykin/HTR2a-bioactivity-prediction

ML Prediction of bioactivity from chemical structure using Morgan Fingerprints /Murcko clustering (target: 5-HT2a receptor)

Language: Jupyter Notebook - Size: 4.95 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 1

Gillingham-Lab/DECL-Gen

DECL-Gen is a toolkit for DNA encoded library to provide the ability to create combinatorial libraries *in situ* and to easily evaluate next generation sequencing results comming from library enrichments.

Language: Python - Size: 207 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 6 - Forks: 3

mathcom/MTMR

MTMR: Molecule-to-Molecule Translation using Metric Learning and Reinforcement Learning (under review)

Language: Jupyter Notebook - Size: 505 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1

yamasakih/docker-compose-django-rdkit

docker-compose + Django + RDKit database cartridge + PostgreSQL

Language: Python - Size: 36.1 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 3

hejops/reaction-smiles

Automatically generate products from reactant SMILES

Language: Python - Size: 84 KB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

wesleybeckner/gains

project that enables molecular design and computational screening of small molecules

Language: Python - Size: 68.8 MB - Last synced at: 4 days ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 2

shenwanxiang/rdkit_summary Fork of dreadlesss/rdkit_summary

rdkit总结与实践

Size: 1.85 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 5 - Forks: 6

Related Keywords

rdkit 189 cheminformatics 70 python 47 chemistry 33 machine-learning 28 chemoinformatics 23 pytorch 17 drug-discovery 16 rdkit-chem 14 bioinformatics 14 computational-chemistry 13 molecule 12 deep-learning 11 scikit-learn 11 drug-design 11 docker 10 smiles 10 postgresql 10 python3 8 openbabel 8 molecules 7 qsar 7 jupyter-notebook 7 pandas 7 molecular-descriptors 6 molecular-fingerprints 6 gnn 6 data-science 5 artificial-intelligence 5 molecule-viewer 5 molecular-dynamics 5 neural-network 5 pytorch-geometric 4 ai 4 jupyter 4 chembl 4 quantum-chemistry 4 cpp 4 materials-informatics 4 chemaxon 4 streamlit 4 data-driven-design 4 ecfp4 4 docking 4 materials-science 4 polymer 4 polymer-informatics 4 medicinal-chemistry 4 chemical-space 3 python-script 3 graph-neural-networks 3 bokeh 3 conformer 3 virtual-screening 3 graph-neural-network 3 sdf 3 networkx 3 fingerprints 3 sklearn 3 rdkit-tutorials 3 docker-image 3 xgboost 3 classification 3 pymol 3 typescript 3 dockerfile 3 react 3 graph-convolutional-networks 3 metabolomics 2 api 2 transformer 2 ligand 2 3d 2 nim-lang 2 molecule-visualization 2 javascript 2 applicability-domain 2 mordred 2 cli 2 nlp 2 tensorflow 2 maccs-fingerprint 2 descriptors 2 molecular-encoding 2 visualization 2 anaconda 2 simulation 2 psi4 2 data-visualization 2 random-forest 2 molecular-dynamics-simulation 2 molecule-generation 2 mdanalysis 2 toxicity 2 cellprofiler 2 pypi-package 2 chemical-informatics 2 machine 2 structure 2 django-rest-framework 2