learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.
not rated 158 today A 27 tokens
original MIT
158Stars on the repository
134Mods indexed here, across every type
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learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Compute RDKit physicochemical descriptors and rule-based drug-likeness heuristics (Ro5, Veber, QED) from SMILES.
not rated 158 today A 36 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Define a docking search box (center coordinates + box dimensions in Angstroms) from a co-crystal ligand, binding-site residues, or a saved JSON specification. Use this skill whenever the user mentions binding site, docking box, search box, grid box, active site definition, or pocket definition, or needs to specify…
not rated 158 today A 101 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Fetch biological assays and target proteins a chemical has been tested against via PubChem.
not rated 158 today A 23 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Build a solvated, charge-neutralized protein-ligand complex for OpenMM molecular dynamics simulation. Combines a prepared receptor PDB and ligand SDF, parameterizes the ligand with OpenFF Sage or GAFF (AM1-BCC charges), applies Amber ff14SB to the protein, solvates with explicit water, and adds counterions. Use this…
not rated 158 today A 118 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Query ChEMBL web services for targets, molecules, and curated bioactivity measurements (IC50, Ki, EC50, etc.).
not rated 158 today A 33 tokens
original MIT
drug-db-pdb
31learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.
not rated 158 today A 41 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Query PubChem via PUG-REST to retrieve CIDs, computed properties, synonyms, and 2D/3D SDF structures.
not rated 158 today A 35 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Post-docking analysis of virtual screening results including score distributions, enrichment metrics (ROC AUC, enrichment factors), and ligand efficiency calculations.
not rated 158 today A 32 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Dock small-molecule ligands into a protein receptor using AutoDock Vina (Python API) and save ranked poses + docking metadata for reproducible virtual screening.
not rated 158 today A 38 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Prepare small-molecule ligands for docking and analysis via optional state enumeration, 3D conformer generation, MMFF/UFF minimization, and export to SDF + AutoDock PDBQT.
not rated 158 today A 48 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Compute single-trajectory MM-GBSA and / or MM-PBSA binding free energy estimates from a protein-ligand MD trajectory. Two backends: a fast OpenMM GBn2 path (no extra dependencies) and an AmberTools MMPBSA.py path that supports both GB (multiple igb models) and Poisson-Boltzmann PB on the same trajectory.
not rated 158 today A 86 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.
not rated 158 today A 33 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Identify and rank ligandable pockets on a protein structure or model using geometry (fpocket) or an ML predictor (P2Rank). Returns ranked pockets with lining residues, geometric center, volume, and a druggability score per pocket. Excludes docking; pair with drug-binding-site-definition or drug-docking-vina…
not rated 158 today A 111 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Validate docked or generated ligand poses for physical plausibility using PoseBusters, filtering out chemically invalid or clashing poses before downstream refinement.
not rated 158 today A 33 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Run a protein-ligand MD simulation in OpenMM with energy minimization, restrained equilibration, and production NPT, producing trajectory and checkpoint files for downstream analysis.
not rated 158 today A 42 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Prepare macromolecular receptor structures (PDB/mmCIF or RCSB PDB ID) for docking or simulation by fixing common structure issues and adding hydrogens.
not rated 158 today A 41 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Compute symmetry-corrected heavy-atom RMSD between docked poses and a reference crystal ligand to validate docking protocols.
not rated 158 today A 31 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Predict synthetic accessibility and retrosynthetic pathways for novel molecules using the IBM RXN API.
not rated 158 today A 22 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Analyze a protein-ligand MD trajectory to compute ligand RMSD, pocket RMSF, hydrogen bonds, contact occupancy, and protein-ligand interaction fingerprints over time.
not rated 158 today A 39 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Search and retrieve research papers from ArXiv API for scientific research.
not rated 158 today A 19 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.
not rated 158 today A 27 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
not rated 158 today A 25 tokens
original MIT
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Retrieves averaged elemental prices and provides direct vendor purchase links for elements and precursor compounds.
not rated 158 today A 23 tokens
original MIT
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