RDKit

Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.

K-Dense-AI/scientific-agent-skills

Load or backfill the ORD ORM Postgres database and verify it before cutover.

open-reaction-database/ord-schema

把一个化学反应做成自包含的微观 3D 交互演示网页：左/上为 Three.js 可交互分子动画 （拖滑块看断键·成键·原子重组，分步高亮），右为 KaTeX 反应方程 + 分步讲解 + 原子守恒计数 + 可选能量-反应进程曲线。支持三入口——给定文字反应/方程、随机出题、上传图片识别后演示。

wy51ai/edulab

Design and run computational protein and ligand workflows on a GPU: binder and enzyme design, de novo backbone generation, inverse folding and sequence redesign, structure prediction, protein-ligand…

locbp-uzh/biopipelines

Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails.

jinzhezenggroup/computational-chemistry-agent-skills

Computes RDKit physicochemical descriptors and molecular fingerprints from SMILES through a uv-run CLI script that skips and logs invalid molecules.

jinzhezenggroup/computational-chemistry-agent-skills

Reference guide for working with molecules in RDKit: reading SMILES and SDF files, computing descriptors and fingerprints, and searching substructures.

aiming-lab/AutoResearchClaw

Cloud-based quantum chemistry platform with Python API. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

Guides molecular work with RDKit in Python: reading SMILES and SDF, sanitization, descriptors, fingerprints, substructure and similarity search, reactions and coordinates.

davila7/claude-code-templates

RDKit molecular manipulation and visualization within Coot's Python environment.

pemsley/coot

A standardized CLI wrapper for Uni-Mol molecular ML workflows that handles representation extraction (embeddings), model training (regression/classification), and property prediction with built-in…

jinzhezenggroup/computational-chemistry-agent-skills

3Dmol.js WebGL molecular visualization emitted as self-contained HTML.

jaechang-hits/SciAgent-Skills

Pythonic wrapper around RDKit with simplified interface and sensible defaults.

davila7/claude-code-templates

Read, write, and edit ChemDraw CDX/CDXML files with RDKit's rdkit.Chem.rdChemDraw plus direct XML editing, always paired with a rendered PNG.

jaechang-hits/SciAgent-Skills

Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.

learningmatter-mit/AtomisticSkills

Generate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.

learningmatter-mit/AtomisticSkills

Builds and troubleshoots TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and…

K-Dense-AI/scientific-agent-skills

Write code that calls the installed nvMolKit Python API for GPU-accelerated, batched RDKit-style operations - Morgan fingerprints, Tanimoto/cosine similarity, ETKDG conformer embedding, MMFF/UFF…

NVIDIA-BioNeMo/bionemo-agent-toolkit

Featurizes small molecules with Molfeat for QSAR/QSPR, chemical similarity, virtual screening, and molecular ML.

K-Dense-AI/scientific-agent-skills

A skill your agent uses when writing or debugging nvMolKit Python code for GPU-accelerated RDKit fingerprints, similarity, conformers, clustering, and molecular searches.

NVIDIA/skills

Build molecules with RDKit — from SMILES or a scaffold, analogues and series (each with its parent), properties (MW, cLogP, TPSA, Lipinski, Veber, QED, alerts), similarity and substructure search…

autonomous-ai/openharness

Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape)…

GPTomics/bioSkills

Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, product…

GPTomics/bioSkills

Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape +…

GPTomics/bioSkills

Searches molecular libraries for substructure matches using SMARTS patterns with explicit handling of recursive SMARTS, ring membership, aromaticity dialect, vector binding, atom map indices, and…

GPTomics/bioSkills

Run predictions with a finetuned KERMT checkpoint on a SMILES-only CSV.

NVIDIA/skills

Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware…

GPTomics/bioSkills

Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain…

GPTomics/bioSkills

Predicts absorption, distribution, metabolism, excretion and toxicity for drug candidates with ADMETlab 3.0, ADMET-AI, DeepChem and chemprop, plus druglikeness filters.

GPTomics/bioSkills

Designs covalent inhibitors and warheads targeting cysteine, lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide…

GPTomics/bioSkills

Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using RDKit and Open Babel with rigorous handling of aromaticity perception…

GPTomics/bioSkills

Standardizes molecular structures using the ChEMBL structure pipeline for normalization and parent selection plus RDKit rdMolStandardize for explicit custom steps such as tautomer canonicalization…

GPTomics/bioSkills

Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al.

GPTomics/bioSkills

Validates docked / generated protein-ligand poses using PoseBusters physical-validity tests, strain energy quantification, geometric checks (planarity, vdW overlap, bond/angle distortion), and…

GPTomics/bioSkills

Dock small-molecule guests into a porous host material using the VOID library (Voronoi Clustering), generating multiple 3D conformers with RDKit and ranking generated complexes.

learningmatter-mit/AtomisticSkills

Molecular docking with AutoDock Vina (Python API). An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Molecular featurization hub (100+ featurizers) for ML. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure…

jaechang-hits/SciAgent-Skills

Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models.

FreedomIntelligence/OpenClaw-Medical-Skills

Calculates molecular descriptors and fingerprints using RDKit.

FreedomIntelligence/OpenClaw-Medical-Skills

Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel.

FreedomIntelligence/OpenClaw-Medical-Skills

Enumerates chemical libraries through reaction SMARTS transformations using RDKit.

FreedomIntelligence/OpenClaw-Medical-Skills

Performs molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit.

FreedomIntelligence/OpenClaw-Medical-Skills

Searches molecular libraries for substructure matches using SMARTS patterns with RDKit.

FreedomIntelligence/OpenClaw-Medical-Skills

Pythonic RDKit wrapper with sensible defaults for drug discovery.

jaechang-hits/SciAgent-Skills

Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings.

jaechang-hits/SciAgent-Skills

NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus.

majiayu000/claude-skill-registry

Computational chemistry workflow guide for DeepChem, PySCF, RDKit, assay-table normalization, PDBbind-style structure datasets, QSAR and structure benchmarks, DrugBank lookup, ligand-only and…

DrugClaw/DrugClaw