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An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with chemoinformatics

A curated list of projects in awesome lists tagged with chemoinformatics .

https://github.com/k-dense-ai/scientific-agent-skills

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 138 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Antigravity, and the open Agent Skills standard.

agent-skills ai-scientist bioinformatics chemoinformatics claude claude-skills claudecode clinical-research computational-biology data-analysis drug-discovery genomics materials-science metabolomics proteomics scientific-computing scientific-visualization

Last synced: 28 May 2026

https://github.com/chembl/chembl_webresource_client

Official Python client for accessing ChEMBL API

chembl cheminformatics chemistry chemoinformatics python rest rest-client

Last synced: 21 Oct 2025

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: 17 Apr 2025

https://github.com/jajupmochi/graphkit-learn

A python package for graph kernels, graph edit distances, and graph pre-image problem.

chemoinformatics graph-edit-distance graph-kernels graph-representations kernel-methods machine-learning paths pattern-recognition pre-image walks

Last synced: 01 May 2025

https://github.com/topazape/lstm_chem

Implementation of the paper - Generative Recurrent Networks for De Novo Drug Design.

cheminformatics chemoinformatics denovo keras lstm machine-learning python3 rnn tensorflow2

Last synced: 13 Apr 2025

https://github.com/drrdom/pmapper

3D pharmacophore signatures and fingerprints

chemoinformatics pharmacophore

Last synced: 19 Feb 2026

https://github.com/MolecularAI/DockStream

DockStream: A Docking Wrapper to Enhance De Novo Molecular Design

astrazeneca chemoinformatics denovo-design jupyter-notebook molecular-docking reinforcement-learning

Last synced: 09 May 2025

https://github.com/OSU-NLP-Group/ScienceAgentBench

[ICLR'25] ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery

ai4science bioinformatics chemoinformatics code-generation cognitive-neuroscience geoscience language-agent large-language-models task-automation

Last synced: 14 Oct 2025

https://github.com/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.

chemoinformatics gc-ms gcxgc kegg lc-ms lipidomics maldi mass-spectrometry metabolomics metadna ms-dial ms-imaging mzkit r-sharp raman-spectroscopy single-cell single-cell-metabolism visualbasic

Last synced: 19 Feb 2026

https://github.com/topazape/molecular-vae

Implementation of the paper - Automatic chemical design using a data-driven continuous representation of molecules

cheminformatics chemoinformatics denovo machine-learning python3 pytorch vae

Last synced: 20 Jul 2025

https://github.com/arpitnarechania/d3-molecule

D3 based interactive visualization library + tool to make render atoms and molecules learning chemical bonding in a fun way.

atoms-in-molecules chemical-bonding chemoinformatics d3 interactive-visualizations javascript molecules open-source

Last synced: 27 Oct 2025

https://github.com/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

Last synced: 14 Apr 2025

https://github.com/ci-lab-cz/pharmd

MD pharmacophores and virtual screening

chemoinformatics pharmacophore-models

Last synced: 16 Jan 2026

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: 23 Oct 2025

https://github.com/paccmann/paccmann_datasets

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

bioinformatics chemoinformatics deep-learning python pytorch rdkit smiles

Last synced: 09 Apr 2025

https://github.com/metgem/metgem

Calculation and visualization of molecular networks based on t-SNE algorithm

chemistry chemoinformatics cosine-similarity graph mass-spectrometry metabolomics network networking

Last synced: 12 Apr 2025

https://github.com/unixjunkie/smi2sdf3d

3D diverse conformers generation using rdkit

3d chemoinformatics conformer ligand python-script rdkit sdf smi smiles

Last synced: 14 Apr 2025

https://github.com/longemen3000/ChemicalIdentifiers.jl

chemical identifiers (CAS, PubChemID, SMILES,InChI, InChI keys, names) from text search

cas chemical-identifiers chemistry chemoinformatics identifiers inchi inchi-key pubchem smiles

Last synced: 06 Apr 2025

https://github.com/longemen3000/chemicalidentifiers.jl

chemical identifiers (CAS, PubChemID, SMILES,InChI, InChI keys, names) from text search

cas chemical-identifiers chemistry chemoinformatics identifiers inchi inchi-key pubchem smiles

Last synced: 28 Jul 2025

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: 14 Apr 2025

https://github.com/unixjunkie/acpc

Chemoinformatics tool for ligand-based virtual screening

chemoinformatics lbvs ligand ocaml partial-charges

Last synced: 14 Apr 2025

https://github.com/chembl/compound_target_pairs_dataset

Automatic extraction of interacting compound-target pairs from ChEMBL.

chembl cheminformatics chemistry chemoinformatics dataset drug-target-interactions drug-targets python

Last synced: 11 Feb 2026

https://github.com/osu-nlp-group/scienceagentbench

ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery

ai4science bioinformatics chemoinformatics code-generation cognitive-neuroscience geoscience language-agent large-language-models task-automation

Last synced: 26 Apr 2025

https://github.com/paccmann/paccmann_gp

PyTorch/skopt based implementation of Bayesian optimization with Gaussian processes - build to optimize latent spaces of VAEs to generate molecules with desired properties

bayesian-optimization chemoinformatics gaussian-processes generative-model machine-learning

Last synced: 10 Apr 2025

https://github.com/fkaiserbio/fit3d

🔍 Fit3D - An application for template-based detection of small structural motifs in protein structures and macromolecular structure data.

bioinformatics chemoinformatics protein-structure

Last synced: 11 Apr 2025

https://github.com/scipion-chem/scipion-chem

Base Scipion plugin defining objects and protocols for CHEMoinformatics

base chemoinformatics modelling protein-structure scipion

Last synced: 14 Jan 2026

https://github.com/tinaccil/isomers_generator

Python code for generating all the possible molecules starting from a chemical formula

chemistry chemoinformatics isomers reaction-networks

Last synced: 29 Apr 2025

https://github.com/unixjunkie/consent

ligand-based virtual screening with consensus queries

chemical chemoinformatics consensus ecfp4 fingerprint lbvs ligand maccs molprint2d ocaml

Last synced: 06 Oct 2025

https://github.com/cbouy/molhighlighter

Multicolored substructure highlights made easy

cheminformatics chemistry chemoinformatics rdkit

Last synced: 28 Oct 2025

https://github.com/unixjunkie/hts_shrink

Reference implementation of the Distance-Based Boolean Applicability Domain for HTS datasets

applicability-domain bandwidth-selection cadd chemoinformatics hts lbvs ocaml-program parzen-window qsar sample-selection

Last synced: 14 Apr 2025

https://github.com/unixjunkie/chemoinfo_recipes

Command line recipes for the working chemoinformatician

chemaxon chemoinformatics howto ligand openbabel rdkit rmsd

Last synced: 05 Jan 2026

https://github.com/fkaiserbio/mmm

⚒️ Macromolecular Miner - A framework for template-free detection of substructure conservation in biological structure data.

bioinformatics chemoinformatics protein-structure

Last synced: 27 Jun 2025

https://github.com/akuroiwa/chem-ant

Select materials to output molecules similar to the target molecule with MCTS Solver and Genetic Programming.

cheminformatics chemoinformatics deap genetic-programming mcts-solver rdkit

Last synced: 17 Jan 2026

https://github.com/zmactep/smiles

Full support of OpenSMILES specification for Haskell

chemoinformatics haskell parser smiles

Last synced: 10 Apr 2025

https://github.com/unixjunkie/rankers

Reference implementation of the Vanishing Ranking Kernels (VRK) method

applicability-domain bandwidth-selection cadd chemoinformatics classification hts kde lbvs ocaml-program qsar vrk

Last synced: 14 Apr 2025

https://github.com/stefan-schroedl/molecule_classification

"Auto-sklearn for chemistry" - train and run machine-learned classifiers for molecular classification tasks.

automatic automl cheminformatics chemistry chemoinformatics hyperparameter-optimization machine-learning molecule python rdkit scikit-learn

Last synced: 25 Sep 2025

https://github.com/tinaccil/connectivity_chemical_graph

Python script that permits to encode molecules as molecular graph and compare easily the connectivity of two molecules

chemical-graph chemoinformatics encode-molecules isomorphism

Last synced: 11 Oct 2025

https://github.com/metgem/libmetgem

A library for molecular networking based on MS/MS spectra.

chemistry chemoinformatics cosine-similarity cython mass-spectrometry

Last synced: 28 Oct 2025

https://github.com/tinaccil/fortranthermostats

Molecule thermostatistics properties code in Fortran90

chemoinformatics molecule thermodynamics

Last synced: 02 Feb 2026

https://github.com/adam-maz/cns_mpo_calculator

Here I provide some code that enables users to calculate CNS MPO score for their molecules, based on the SMILES and known pKa values.

chemoinformatics cnsmpo computer-aided-drug-design descriptors filter medicinal-chemistry object-oriented-programming python rdkit virtual-screening

Last synced: 01 Mar 2026

https://github.com/Marta-Barea/visnir-waxtype-classification-ml

Spectroscopic data processing approaches for petroleum wax discrimination

cheminformatics chemistry chemoinformatics machine-learning petroleum r vis-nir-spectroscopy

Last synced: 07 Apr 2025

https://github.com/unixjunkie/pychem

backup copy of https://code.google.com/archive/p/pychem/downloads

chemoinformatics molecular-descriptors

Last synced: 26 Mar 2025

https://github.com/unixjunkie/lbvs_no_decoys

Two datasets for Ligand-Based Virtual Screening benchmarking without decoys

chemoinformatics dataset lbvs

Last synced: 19 Mar 2026

https://github.com/marta-barea/visnir-waxtype-classification-ml

Spectroscopic data processing approaches for petroleum wax discrimination

cheminformatics chemistry chemoinformatics machine-learning petroleum r vis-nir-spectroscopy

Last synced: 13 Feb 2026

https://github.com/xiaohuang-6/rl-llm-genai-egfr-de-novo-small-drug-molecule

ChemBERTa + RL pipeline for de novo EGFR inhibitor design with docking validation.

chemoinformatics docking drug-discovery machine-learning reinforcement-learning smiles transformers

Last synced: 18 May 2026

https://github.com/ethanbass/vpdtw

Variable Penalty Dynamic Time Warping

chemoinformatics chemometrics chromatography time-series time-warping

Last synced: 05 Apr 2025

https://github.com/prospero1988/nmr-ai_part3

Machine learning and neural network models for CHI logD prediction based on ¹H and ¹³C NMR spectral data. Supplementary code for the third paper in the "From NMR to AI" series.

chemoinformatics cnn logd machine-learning mlflow mlp neural-network nmr nmr-spectroscopy optuna python3 pytorch regression svr xgboost

Last synced: 19 Apr 2026

https://github.com/laura-budurlean/drug-discovery-with-python-and-machine-learning

Explore data collection, analysis, and machine learning for drug discovery. Create predictive models, perform EDA, and deploy as web apps.

biochemistry bioinformatics biostatistics biotechnology chemoinformatics computational-biology drug-discovery machine-learning pharmacokinetics pharmacology python qsar-modeling sklearn webapp

Last synced: 02 May 2026

https://github.com/hiroyokoyama/python_molecular_editor

MoleditPy -- A cross-platform, simple, and intuitive molecular editor built in Python. Please note that these codes are written with the assistance of LLM.

chemistry-education chemistry-lab chemoinformatics

Last synced: 09 Apr 2026

https://github.com/raghavagps/raghavagps.github.io

Home Page of Prof G P S Raghava, group work in the field of bioinformatics, chemoinformatics and pharmacoinformatics. Mainly developed databases and prediction methods using machine learning techniques

bioinformatics chemoinformatics computer-aided machine-learning-algorithms pharmacometrics

Last synced: 31 Oct 2025

https://github.com/dhimmel/unichem

A python package for mapping compounds via UniChem

chemical chemoinformatics compounds fikhb mapping rephetio unichem

Last synced: 23 Mar 2025

https://github.com/yonghuidong/msbox

Tools for Metabolomics and mass Spectrometry users

chemoinformatics mass-spectrometry metabolites metabolomics

Last synced: 22 Oct 2025

https://github.com/cbouy/m2-chemoinformatics

Scripts I used during my Master in Chemoinformatics in Strasbourg

bash chemoinformatics scripting

Last synced: 18 May 2026

https://github.com/marta-barea/visnirs-wax-mixture-regression

Spectroscopic data processing approaches for petroleum wax blends quantification

chemistry chemoinformatics chemometrics machine-learning petroleum r

Last synced: 20 Oct 2025

https://github.com/noedemange/m2amisprojet-graphedecycles

Comparaison des graphes de cycles des molécules par calcul de la similarité par MCIS et par distance de Levenshtein

chemoinformatics levenshtein-distance mcis molecule similarity

Last synced: 20 Jan 2026

https://github.com/emapco/chem-mrl

Chem-MRL: SMILES Matryoshka Representation Learning Embedding Model

chemoinformatics embedding-models latent-space matryoshka-representation-learning smiles

Last synced: 01 May 2025

https://github.com/scipion-chem/scipion-chem-modeller

Plugin for using modeller software inside scipion.

chemoinformatics scipion

Last synced: 17 Jan 2026

https://github.com/scipion-chem/scipion-chem-durrantlab

Scipion-chem plugin for Durrant Lab software

chemoinformatics durrantlab scipion

Last synced: 17 Jan 2026

https://github.com/tinaccil/fromgraphtoxyz

Script to help in the creation of molecules xyz file from molecular graph (i.e. only connectivity).

chemical-graph chemoinformatics molecule

Last synced: 14 May 2026

https://github.com/scipion-chem/scipion-chem-openmm

Plugin for OpenMM software

chemoinformatics openmm scipion

Last synced: 17 Jan 2026

https://github.com/andschar/chemlook

An R Package and Database containing Information on Chemicals

biology chemistry chemoinformatics database r

Last synced: 27 Apr 2026

https://github.com/Marta-Barea/visnirs-wax-mixture-regression

Spectroscopic data processing approaches for petroleum wax blends quantification

chemistry chemoinformatics chemometrics machine-learning petroleum r

Last synced: 07 Apr 2025

https://github.com/tinaccil/gretobape_cleaning

Cleaning Astrochemical Reaction network via Thermodynamics principles

astrochemistry chemoinformatics graph networks quantum-chemistry reaction-network

Last synced: 27 Feb 2025

https://github.com/brsynth/molecule-signature

Signature based molecule enumeration from morgan fingerprints

chemoinformatics fingerprint generative-ai synthetic-biology

Last synced: 16 Jan 2026

https://github.com/brsynth/molecule-signature-paper

Code supporting the paper 'Getting Molecules from their Fingerprints: Generative Models vs. Deterministic Enumeration'

chemistry chemoinformatics deterministic-enumeration fingerprint generative-model molecular-generation signature

Last synced: 16 Jan 2026

https://github.com/kyllev/smiles-mapper

Small web-app allowing interactive vizualization of how chemical string and files like SMILES, InChi and .mol/.sdf are created

chemistry chemoinformatics inchi inchi-string molecule smiles smiles-strings visualization

Last synced: 06 Apr 2025

https://github.com/marta-barea/tic-hs-gc-ims-waters-ml

Machine learning-based analytical approach for processing TIC data from contaminated water samples with PDPs, obtained through HS-GC-IMS

analytical-chemistry chemistry chemoinformatics chemometrics chromatography headspace ims machine-learning machine-learning-algorithms petroleum waters

Last synced: 24 Feb 2025

https://github.com/adam-maz/multimodal-fcnn-classifier

Here we provide fCNN, multimodal small drug screening toolkit based on Morgan fingerprints and images of simulated (Docking, DFT) molecules.

5-ht6 chemoinformatics cnn dft-calculations fingerprints medicinal-chemistry molecular-docking multimodal-deep-learning transfer-learning virtual-screening

Last synced: 08 Oct 2025

https://github.com/marta-barea/visnir-paraffinwax-hydroprocessing-ml

Repository for analyzing paraffin wax using Vis-NIR and machine learning techniques to assess hydroprocessing.

chemoinformatics machine-learning petroleum r rstudio vis-nir-spectroscopy

Last synced: 26 Oct 2025

https://github.com/yoannpa/initiation_chemoinformatics

Small initiation in Python to learn how to work with fingerprints files.

chemoinformatics fingerprints-files initiation-chemoinformatics jupyter-notebook python

Last synced: 17 May 2026