learningmatter-mit
- 130 skills
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- ▌ Mat Synthesis Extraction · learningmatter-mit bundleExtract structured synthesis procedures from a folder of PDFs using the LeMat-Synth GeneralSynthesisOntology schema, producing one JSON file per paper with per-material synthesis records.
- ▌ Ml Bayesian Optimization · learningmatter-mit bundleIteratively optimize expensive black-box objectives — such as materials properties, experimental yields, or simulation outputs — by learning from past evaluations to select the most promising next candidates.
- ▌ Ml Committee Uncertainty · learningmatter-mit bundleQuantify prediction uncertainty of MACE MLIPs using committee (ensemble) models; flag high-uncertainty structures for DFT verification.
- ▌ Ml Foundation Potentials · learningmatter-mitGuide for selecting the most appropriate foundation MLIP model based on simulation requirements.
- ▌ Chem Dft Orca Singlepoint · learningmatter-mit bundleRun a DFT or Coupled Cluster single-point energy calculation (with optional gradients/Hessian) on a molecular structure with ORCA through SCINE wrapper.
- ▌ Mat Calphad Phase Diagram · learningmatter-mit bundleCalculate and plot multi-component temperature-composition phase diagrams from Thermodynamic Database (.tdb) files using CALPHAD methods.
- ▌ Mat Intercalation Voltage · learningmatter-mit bundleCalculate the average intercalation voltage of cathode materials using MLIPs.
- ▌ Mat Qha Thermal Expansion · learningmatter-mit bundleCalculate Quasi-Harmonic Approximation (QHA) thermal properties using MLIPs.
- ▌ Chem Dft Orca Optimization · learningmatter-mit bundleRun DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.
- ▌ Mat Dft Mixing Functionals · learningmatter-mit bundleEnergy corrections needed when using certain MLIPs for phase diagram construction / formation energy calculations.
- ▌ Mat Electrochemical Window · learningmatter-mit bundleCalculate the intrinsic electrochemical stability window (ECW) of a material using standard phase diagram thermodynamic methods.
- ▌ Mat Md Probability Density · learningmatter-mit bundleCalculate and visualize the probability density of diffusing ions from a Molecular Dynamics (MD) trajectory.
- ▌ Drug Complex System Builder · learningmatter-mit bundleBuild 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 skill when the user wants to solvate a complex, set up a system for MD, prepare for simulation, add water and ions, or build a simulation box from a protein-ligand structure.
- ▌ Drug Molecular Fingerprints · learningmatter-mit bundleCompute Morgan/ECFP fingerprints, Tanimoto similarity, and optional Butina clusters/heatmaps for small-molecule comparison.
- ▌ General Chemical Literature · learningmatter-mit bundleRetrieve extensive literature (PubMed) and patent associated with a specific chemical compound via PubChem.
- ▌ Mat Random Structure Search · learningmatter-mit bundleGenerate random crystal structures for a given composition (AIRSS-style) and relax with MLIPs to find low-energy candidates.
- ▌ Mat Dielectric Response · learningmatter-mit bundleCalculate frequency-dependent dielectric response using atomate2 OpticsMaker and VASP.
- ▌ Mat Kinetic Monte Carlo · learningmatter-mit bundleSimulate long-time kinetics using rejection-free kinetic Monte Carlo (KMC) with event catalog construction, rate assignment via TST/Arrhenius, detailed-balance validation, superbasin handling, and transport analysis.
- ▌ Ml Generative Mattergen · learningmatter-mit bundleGenerate inorganic material structures using MatterGen, a diffusion-based generative model.
- ▌ Ml Property Predict Scd · learningmatter-mit bundleTrain a model to predict custom properties of molecules or periodic materials using pretrained SelfConditionedDenoisingAtoms (SCD) foundation models.
- ▌ Drug Trajectory Analysis · learningmatter-mit bundleAnalyze a protein-ligand MD trajectory to compute ligand RMSD, pocket RMSF, hydrogen bonds, contact occupancy, and protein-ligand interaction fingerprints over time.
- ▌ General Chemical Pricing · learningmatter-mit bundleRetrieves averaged elemental prices and provides direct vendor purchase links for elements and precursor compounds.
- ▌ General Fair Data Review · learningmatter-mitReview a manuscript or code repository for FAIR data compliance (Findable, Accessible, Interoperable, Reusable), producing a structured report with pass/fail per principle and actionable remediation steps.
- ▌ General Workflow Planner · learningmatter-mit bundleHierarchically decompose high-level scientific workflows (from literature or user-proposed) into executable sequences of existing SKILLs and MCP tools for the research plan.
- ▌ Mat Electronic Structure · learningmatter-mit bundleCalculate electronic band structure and density of states using atomate2 and VASP.
- ▌ Drug Binding Site Definition · learningmatter-mit bundleDefine 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 where to dock ligands on a protein. Also use when the user has a protein target but needs help figuring out where to dock before running a docking skill.
- ▌ Mat Calphad Property Diagram · learningmatter-mit bundleCalculate temperature-dependent thermodynamic properties like Equilibrium Phase Fractions for a specific alloy composition using CALPHAD models.
- ▌ Mat Dft Electronic Transport · learningmatter-mit bundleCompute electronic transport properties (mobility, conductivity, Seebeck coefficient) using DFT and AMSET via atomate2.
- ▌ Mat Phase Field Conservative · learningmatter-mit bundleSimulate conservative phase-fields (spinodal decomposition and phase separation) using the Cahn-Hilliard equation.
- ▌ Mat Synthesis Recommendation · learningmatter-mit bundleQuery and rank synthesis recipes from Materials Project's text-mined literature database with precursors, procedures, and journal references.
- ▌ Mat Lattice Thermal Conductivity · learningmatter-mit bundleCalculate lattice thermal conductivity of materials with MLIPs.
- ▌ Mat Phase Field Non Conservative · learningmatter-mit bundleSimulate non-conservative phase-fields (grain growth and phase transformations) using the Allen-Cahn equation.
- ▌ General Query Literature Database · learningmatter-mitFind relevant simulation workflows in the in-house literature database.
- ▌ Chem Dft Orca Advanced Calculation · learningmatter-mit bundleWrite and run custom ORCA input files for advanced electronic structure methods or settings not available through the SCINE wrapper, including multi-reference methods, excited states, relativistic effects, advanced SCF, NMR/EPR, and more.
- ▌ Mat Grand Canonical Mc · learningmatter-mit bundleRun Grand Canonical Monte Carlo (GCMC) simulations with cluster expansion models to map composition-temperature phase diagrams via chemical potential sweeps.
- ▌ Mat Ionic Substitution · learningmatter-mit bundleDiscover new crystal structures by data-mined ionic substitution — propose candidates from existing structures (forward) or find potential structures for a target composition (reverse).
- ▌ Mat Surface Adsorption · learningmatter-mit bundleCalculate surface adsorption energies for adsorbate-surface combinations using MLIPs.
- ▌ Mat Xrd Phase Analysis · learningmatter-mit bundlePhase identification from experimental XRD using DARA's tree search (Ray-based).
- ▌ General Publisher Access Guard · learningmatter-mit bundleAvoid bot-blocking publisher websites by routing paper retrieval through legal open-access APIs and mirrors.
- ▌ Mat Dft Electron Phonon · learningmatter-mit bundleComputes electron-phonon coupling to calculate temperature-dependent bandgap renormalization using atomate2.
- ▌ Drug Admet Prediction · learningmatter-mit bundleCompute RDKit physicochemical descriptors and rule-based drug-likeness heuristics (Ro5, Veber, QED) from SMILES.
- ▌ Drug Docking Analysis · learningmatter-mit bundlePost-docking analysis of virtual screening results including score distributions, enrichment metrics (ROC AUC, enrichment factors), and ligand efficiency calculations.
- ▌ Drug Pocket Detection · learningmatter-mit bundleIdentify 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 downstream. Use whenever the user has a protein but no binding-site information, asks about cryptic / allosteric / orphan pockets, needs to assess druggability, or wants to choose where to dock.
- ▌ General Deep Research · learningmatter-mitPerform iterative, deep, and comprehensive literature research on a specific materials/chemistry topic.
- ▌ General Patent Search · learningmatter-mit bundleSearch for patents by keyword, material name, or assignee using free data sources (Google Patents).
- ▌ Mat Epw Mobility · learningmatter-mit bundleCompute phonon-limited carrier mobility and mode-resolved electron-phonon coupling in 2D materials from first principles with Quantum ESPRESSO and EPW.
- ▌ Ml Mace Finetune · learningmatter-mit bundleFine-tune MACE machine learning interatomic potentials on custom datasets.
- ▌ Chem Docking Void · learningmatter-mit bundleDock small-molecule guests into a porous host material using the VOID library (Voronoi Clustering), generating multiple 3D conformers with RDKit and ranking generated complexes.
- ▌ Chem Msms Predict · learningmatter-mit bundlePredict LC-MS/MS (MS2, tandem mass spectra) from SMILES via ICEBERG, a two-stage deep neural network. Outputs predicted m/z vs intensity spectrum, fragment ion SMILES, and a spectrum plot.
- ▌ Chem Nmr Analysis · learningmatter-mit bundleScripts for Wasserstein deconvolution of 1H NMR mixture spectra against reference spectra, reaction product prediction, time-series kinetics, and spectral plotting.
- ▌ Drug Docking Vina · learningmatter-mit bundleDock small-molecule ligands into a protein receptor using AutoDock Vina (Python API) and save ranked poses + docking metadata for reproducible virtual screening.
- ▌ Chem Similarity Search · learningmatter-mit bundleFind structurally similar chemical compounds using PubChem's 2D fast similarity engine via the PUG-REST API.
- ▌ Drug Bioactivity Assay · learningmatter-mit bundleFetch biological assays and target proteins a chemical has been tested against via PubChem.
- ▌ Drug Protein Ligand Md · learningmatter-mit bundleRun a protein-ligand MD simulation in OpenMM with energy minimization, restrained equilibration, and production NPT, producing trajectory and checkpoint files for downstream analysis.
- ▌ General Biorxiv Search · learningmatter-mit bundleSearch and retrieve preprint metadata from bioRxiv and medRxiv APIs for biological and medical research.
- ▌ General Plot Digitizer · learningmatter-mit bundleExtract continuous X-Y data from experimental spectrum images (Raman, XRD, UV-Vis, IR, etc.) via hybrid VLM + CV pipeline and agent-in-the-loop workflow.
- ▌ Chem TS Optimization · learningmatter-mit bundleOptimize non-periodic molecular TS guesses and verify first-order saddle point from vibrational modes.
- ▌ Drug Pose Validation · learningmatter-mit bundleValidate docked or generated ligand poses for physical plausibility using PoseBusters, filtering out chemically invalid or clashing poses before downstream refinement.
- ▌ General Arxiv Search · learningmatter-mit bundleSearch and retrieve research papers from ArXiv API for scientific research.
- ▌ General Presentation · learningmatter-mit bundleGenerate and iteratively refine PowerPoint presentations from simulation results using python-pptx.
- ▌ Mat Magnetic Density · learningmatter-mit bundleCalculate magnetic moments and spin density from spin-polarized DFT calculations using VASP.
- ▌ Mat Pourbaix Diagram · learningmatter-mit bundleCalculate Pourbaix (pH-voltage) diagrams for aqueous electrochemical stability using water-corrected MLIP energies and pymatgen.
- ▌ Drug Protein Prep · learningmatter-mit bundlePrepare macromolecular receptor structures (PDB/mmCIF or RCSB PDB ID) for docking or simulation by fixing common structure issues and adding hydrogens.
- ▌ Mat Amorphization · learningmatter-mit bundleGenerate amorphorized structures from crystalline starting points using a melt-quench MD protocol.
- ▌ Mat DB Nist Janaf · learningmatter-mit bundleQuery the NIST Chemistry WebBook (which includes JANAF thermochemical tables) for standard experimental thermochemistry properties.
- ▌ Mat Defect Energy · learningmatter-mit bundleCalculate point-defect formation energies (vacancies, substitutions, interstitials) using MLIPs.
- ▌ Mat Melting Point · learningmatter-mit bundleCalculate the melting temperature of a material using the solid-liquid interface (coexistence) method.
- ▌ Mat Phase Diagram · learningmatter-mit bundleRetrieve and visualize pre-computed phase diagrams from Materials Project for thermodynamic stability analysis.
- ▌ General Property Units · learningmatter-mitReference guide for energy, force, and stress units across MLIPs, DFT codes, and ASE, including conversion factors.
- ▌ Mat Diffusion Analysis · learningmatter-mit bundleCalculate ionic diffusion coefficients and activation energy from MD trajectories using pymatgen.
- ▌ Mat Elemental Energies · learningmatter-mit bundleA library of ground-state element structures and their energies calculated from MLIPs. Used to calculate formation energies of compounds.
- ▌ Mat Reaction Network · learningmatter-mit bundlePredict thermodynamically optimal solid-state inorganic synthesis pathways and tabulates basic reactions.
- ▌ Mat Sample Pes By Md · learningmatter-mit bundleSample off-equilibrium potential energy surface (PES), used for benchmarking and fine-tuning MLIPs.
- ▌ Ml Cluster Expansion · learningmatter-mit bundletrain a Cluster Expansion (CE) for lattice-based Monte Carlo simulation of disordered materials.
- ▌ Ml Fairchem Finetune · learningmatter-mit bundleFine-tune Fairchem machine learning interatomic potentials (UMA, ESEN) on custom datasets.
- ▌ Chem Conformer Search · learningmatter-mit bundleGenerate molecular conformers with RDKit ETKDG, relax with MLIPs, and rank by energy with Boltzmann weighting.
- ▌ Chem Irc Verification · learningmatter-mit bundleVerify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.
- ▌ Chem Spectrum Matcher · learningmatter-mit bundleMatch an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation. Supports local catalog lookup, public database fallback, and pluggable similarity metrics.
- ▌ General Peer Review · learningmatter-mit bundleAct as a reviewer to critically review research plans, manuscripts, or task summaries, pointing out missing baselines, statistical flaws, and weak assumptions.
- ▌ Chem Hazard Toxicity · learningmatter-mit bundleExtract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.
- ▌ Chem Thermochemistry · learningmatter-mit bundleCompute gas-phase thermodynamic quantities (H, S, G) and reaction thermochemistry (ΔH, ΔS, ΔG) using MLIPs with the ideal-gas/rigid-rotor/harmonic-oscillator approximation.
- ▌ Mat Dft Lobster · learningmatter-mit bundleConstruct computational flows for VASP electronic structure projection via LOBSTER to calculate chemical bonding insights (COHP, atomic charges, DOS).
- ▌ Mat Md Monitors · learningmatter-mitReal-time monitoring tools for stability, equilibration, and diffusion during ASE molecular dynamics simulations.
- ▌ Chem Neb Barrier · learningmatter-mit bundleCalculate activation barrier using Nudged Elastic Band (NEB) method with MLIPs.
- ▌ Chem Nmr Predict · learningmatter-mit bundlePredict 1H NMR spectra from SMILES strings via NMRdb.org SPINUS neural network prediction and nmrsim quantum mechanical spin simulation.
- ▌ Chem Solution Md · learningmatter-mit bundleSet up and run molecular dynamics simulations of molecules in explicit solvent boxes using Packmol for box construction and MLIPs for dynamics.
- ▌ Drug Ligand Prep · learningmatter-mit bundlePrepare small-molecule ligands for docking and analysis via optional state enumeration, 3D conformer generation, MMFF/UFF minimization, and export to SDF + AutoDock PDBQT.
- ▌ Drug Mmpbsa Gbsa · learningmatter-mit bundleCompute 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.
- ▌ Mat Edi Mobility · learningmatter-mit bundleCompute defect-limited carrier mobility and electron-defect scattering matrix elements in 2D and 3D semiconductors from first principles with Quantum ESPRESSO and the EDI plugin.
- ▌ Mat Defect Energy Dft · learningmatter-mit bundleCalculate charged defect formation energies and transition level diagrams using pymatgen-analysis-defects and atomate2 VASP workflows.
- ▌ Mat Dft Ferroelectric · learningmatter-mit bundleCalculate the spontaneous ferroelectric polarization across a non-polar to polar structure transition using the Berry Phase method.
- ▌ Mat Equation Of State · learningmatter-mit bundleCalculate equation of state (bulk modulus, equilibrium volume) using MLIPs.
- ▌ Mat Solid Free Energy · learningmatter-mit bundleCalculate absolute solid Helmholtz free energy, and optional Gibbs free energy, with Frenkel-Ladd switching using portable MLIP wrappers on a pre-equilibrated periodic structure.
- ▌ Mat Structure Novelty · learningmatter-mit bundleDetermine if a given structure matches known experimental or theoretical structures, or compare two user-provided structures.
- ▌ Ml Generative Diffcsp · learningmatter-mit bundleGenerate crystal structures with exact composition control using DiffCSP++ (space group + Wyckoff positions), or unconditionally from trained distributions.
- ▌ Ml Property Predictor · learningmatter-mit bundleTrain a property predictor head on top of a Machine Learning Interatomic Potential (MLIP) backbone (MACE or MatGL) to predict custom intensive or extensive properties from crystal or molecular structures.
- ▌ Chem Bond Dissociation · learningmatter-mit bundleCalculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.
- ▌ Mat DB Mp · learningmatter-mit bundleQuery Materials Project database for crystal structures, computed properties, elastic/magnetic data, and structurally similar materials using the MP API.
- ▌ Mat Phonon · learningmatter-mit bundleCalculate vibrational properties (phonon dispersions, density of states, thermal properties) using MLIPs.
- ▌ Chem DB Mof · learningmatter-mit bundleQuery multiple MOF databases (QMOF via MPContribs; ARC-MOF DB7/Majumdar et al. via Zenodo) and download CIF structures with optional element or identifier filters.