learningmatter-mit

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Calculate vibrational frequencies, normal modes, zero-point energy, and IR spectra of molecules and clusters using MLIPs.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Compute RDKit physicochemical descriptors and rule-based drug-likeness heuristics (Ro5, Veber, QED) from SMILES.

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…

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Fetch biological assays and target proteins a chemical has been tested against via PubChem.

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…

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

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

learningmatter-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.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Query PubChem via PUG-REST to retrieve CIDs, computed properties, synonyms, and 2D/3D SDF structures.

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.

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.

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.

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.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Compute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.

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…

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.

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.

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.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Compute symmetry-corrected heavy-atom RMSD between docked poses and a reference crystal ligand to validate docking protocols.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

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

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.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Search and retrieve research papers from ArXiv API for scientific research.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Search and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Retrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.

learningmatter-mit/AtomisticSkills

Skill Claude CodeCodex

Retrieves averaged elemental prices and provides direct vendor purchase links for elements and precursor compounds.