Best drug discovery and cheminformatics skills, page 3

Query the ChEMBL database for bioactive molecules, targets, bioactivities, and approved drugs; use this when you need to filter by physicochemical properties (e.g., MW, LogP), chemical structure…

aipoch/medical-research-skills

Diffusion-based molecular docking to predict 3D ligand–protein binding poses (blind docking) with confidence scoring; use when you need pose prediction for drug discovery or virtual screening.

aipoch/medical-research-skills

Programmatic access to DrugBank drug and target data; use when you need to download, parse, and analyze DrugBank XML for properties, interactions, pathways, and pharmacology.

aipoch/medical-research-skills

Medicinal chemistry screening filters for compound prioritization; use when you need to apply drug-likeness rules, PAINS/structural alerts, and complexity metrics to triage or optimize libraries.

aipoch/medical-research-skills

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

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

Query the BindingDB drug-target binding affinity database. An agent skill from QSong-github/DrugClaw.

QSong-github/DrugClaw

Query the ChEBI (Chemical Entities of Biological Interest) database.

QSong-github/DrugClaw

Query the UniTox drug toxicity database. An agent skill from QSong-github/DrugClaw.

QSong-github/DrugClaw

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

Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS.

jaechang-hits/SciAgent-Skills

Molecular ML featurization library (100+ featurizers: ECFP, descriptors, ChemBERTa).

lamm-mit/scienceclaw

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

Therapeutics Data Commons (TDC) AI-ready drug discovery datasets.

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

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D…

aipoch/medical-research-skills

Programmatic access to the PubChem database (via PUG-REST API and PubChemPy) for searching chemical compounds, retrieving physicochemical properties, performing structure similarity/substructure…

aipoch/medical-research-skills

Analyze data with smiles-de-salter using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

aipoch/medical-research-skills

A versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D chemical structure images, and preparing or extracting structures for…

jinzhezenggroup/computational-chemistry-agent-skills

A skill your agent uses WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names.

jinzhezenggroup/computational-chemistry-agent-skills

Extracts the most interesting frames from video files for thumbnail compositing.

swyxio/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

Performs structure-based virtual screening using AutoDock Vina 1.2 for molecular docking.

FreedomIntelligence/OpenClaw-Medical-Skills

Predict a molecule's ability to reverse disease states using DLEPS (Disease-Ligand Embedding Projection Score) for drug repositioning and discovery.

InternScience/scp

Predict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network.

learningmatter-mit/AtomisticSkills

Predict 1H NMR spectra from SMILES strings via NMRdb.org SPINUS neural network prediction and nmrsim quantum mechanical spin simulation.

learningmatter-mit/AtomisticSkills

Find structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.

learningmatter-mit/AtomisticSkills

Set up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.

learningmatter-mit/AtomisticSkills

Query ChEMBL web services for targets, molecules, and curated bioactivity measurements (IC50, Ki, EC50, etc.).

learningmatter-mit/AtomisticSkills

Post-docking analysis of virtual screening results including score distributions, enrichment metrics (ROC AUC, enrichment factors), and ligand efficiency calculations.

learningmatter-mit/AtomisticSkills

Dock small-molecule ligands into a protein receptor using AutoDock Vina (Python API) and save ranked poses + docking metadata for reproducible virtual screening.

learningmatter-mit/AtomisticSkills

Prepare small-molecule ligands for docking and analysis via optional state enumeration, 3D conformer generation, MMFF/UFF minimization, and export to SDF + AutoDock PDBQT.

learningmatter-mit/AtomisticSkills

Predict synthetic accessibility and retrosynthetic pathways for novel molecules using the IBM RXN API.

learningmatter-mit/AtomisticSkills

Python API for RCSB PDB 3D structures (search, fetch coordinates, metadata).

lamm-mit/scienceclaw

Query ClinicalTrials.gov API v2 for trial data. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

Pythonic RDKit wrapper with sensible defaults for drug discovery.

jaechang-hits/SciAgent-Skills

Parse local DrugBank XML for drug info, interactions, targets, and properties.

jaechang-hits/SciAgent-Skills

Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS.

jaechang-hits/SciAgent-Skills

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

jaechang-hits/SciAgent-Skills

Query openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement.

jaechang-hits/SciAgent-Skills