isayev
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Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes
Automated tools for the generation of bespoke SMIRNOFF format parameters for individual molecules.
This is the official repo for the paper "LLM-SR" on Scientific Equation Discovery and Symbolic Regression with LLMs
BBBP Explainer is a code to generate structural alerts of blood-brain barrier penetrating and non-penetrating drugs using Local Interpretable Model-Agnostic Explanations (LIME) of machine learning …
SMARTS: 'regular expressions' for chemical structures
Diffusion model based protein-ligand flexible docking method
20+ high-performance LLMs with recipes to pretrain, finetune and deploy at scale.
A Python API for the RCSB Protein Data Bank (PDB)
Official implement of paper "AutoCrawler: A Progressive Understanding Web Agent for Web Crawler Generation"
The BigBind protein-ligand binding dataset (and BayesBind benchmark)
Resources, Code, and Other things I use to teach Cheminformatics.
Dynamic Radii Adjustment for COntinuum Solvation
Free-energy workflow providing absolute binding free energies from short MD and implicit-solvation to assess the stability of docking poses
Novana is a cheminformatics tool that extends the decomposition of molecules into Bemis-Murcko frameworks.
A community-curated list of resources related to self-driving labs that combine hardware automation and artificial intelligence to accelerate scientific discovery.
The aim of this repository is to provide simple tools to help those working with ColabFold BATCH both for pre and post-processing steps.
QSARtuna: QSAR model building with the optuna framework
Algorithmic prediction of protodeboronation rate with pH (published!)
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.