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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/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/cdk/cdk

The Chemistry Development Kit

bioinformatics blueobelisk cheminformatics chemistry code4lib java

Last synced: 02 Aug 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/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/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/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/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://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