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By learningmatter-mit

129 skills found.
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1
1.Drug Binding Site Definition

Define a docking search box (center coordinates + box dimensions in Angstroms) from a co-crystal ligand, binding-site residues, or a saved JSON specification.

learningmatter-mit/AtomisticSkills176—~2.9kAutomated safety check: PassMITtoday
2
2.Drug Complex System Builder

Build a solvated, charge-neutralized protein-ligand complex for OpenMM molecular dynamics simulation.

learningmatter-mit/AtomisticSkills176—~2kAutomated safety check: PassMITtoday
3
3.Drug Pocket Detection

Identify and rank ligandable pockets on a protein structure or model using geometry (fpocket) or an ML predictor (P2Rank).

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4
4.Chem Bond Dissociation

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

learningmatter-mit/AtomisticSkills176—~2.5kAutomated safety check: PassMITtoday
5
5.Chem Conformer Search

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

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6
6.Chem DB Mof

Query multiple MOF databases (QMOF via MPContribs; ARC-MOF DB7/Majumdar et al.

learningmatter-mit/AtomisticSkills176—~1.9kAutomated safety check: PassMITtoday
7
7.Chem DB Qmof

Query the Quantum MOF (QMOF) database via Materials Project's MPContribs platform for DFT-computed properties (bandgap) and optimized crystal structures of Metal-Organic Frameworks.

learningmatter-mit/AtomisticSkills176—~670Automated safety check: PassMITtoday
8
8.Chem DB Spectra

Search and download experimental InfraRed (IR), Mass spectra, and UV-Vis spectra data (JCAMP-DX format) for molecules.

learningmatter-mit/AtomisticSkills176—~529Automated safety check: PassMITtoday
9
9.Chem Dft Orca Advanced Calculation

Write 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…

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10
10.Chem Dft Orca Optimization

Run DFT geometry optimization (minimization or TS search) on a molecular structure using ORCA via SCINE/ReaDuct wrapper.

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11
11.Chem Dft Orca Singlepoint

Run a DFT or Coupled Cluster single-point energy calculation (with optional gradients/Hessian) on a molecular structure with ORCA through SCINE wrapper.

learningmatter-mit/AtomisticSkills176—~1.8kAutomated safety check: PassMITtoday
12
12.Chem Docking Void

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/AtomisticSkills176—~918Automated safety check: PassMITtoday
13
13.Chem Hazard Toxicity

Extract explicit safety warnings, GHS classifications, LD50 toxicity profiles, and acute oral toxicity triage from PubChem PUG VIEW.

learningmatter-mit/AtomisticSkills176—~702Automated safety check: PassMITtoday
14
14.Chem Irc Verification

Verify non-periodic molecular TS connectivity with forward/reverse IRC using endpoint connectivity and RMSD checks.

learningmatter-mit/AtomisticSkills176—~972Automated safety check: PassMITtoday
15
15.Chem Msms Predict

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

learningmatter-mit/AtomisticSkills176—~1.6kAutomated safety check: PassMITtoday
16
16.Chem Neb Barrier

Calculate activation barrier using Nudged Elastic Band (NEB) method with MLIPs.

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17
17.Chem Nmr Analysis

Scripts for Wasserstein deconvolution of 1H NMR mixture spectra against reference spectra, reaction product prediction, time-series kinetics, and spectral plotting.

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18
18.Chem Nmr Predict

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

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19
19.Chem React Ot

Generate transition state structures for chemical reactions using React-OT.

learningmatter-mit/AtomisticSkills176—~914Automated safety check: PassMITtoday
20
20.Chem Similarity Search

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

learningmatter-mit/AtomisticSkills176—~614Automated safety check: PassMITtoday
21
21.Chem Solution Md

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

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22
22.Chem Sorption Gcmc

Calculates gas adsorption isotherms via BVT/GCMC Monte Carlo simulations in a porous framework using MLIP.

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23
23.Chem Sorption Relax

Prepares supercells for porous frameworks based on minimum interplanar distance and relaxes them using standard MLIP relaxation tools.

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24
24.Chem Sorption Widom

Calculates Henry coefficient and heat of adsorption for a gas in a porous framework using Widom insertion with any supported MLIP.

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25
25.Chem Spectrum Matcher

Match an experimental spectrum (1H NMR, 13C NMR, IR) against predicted or database reference spectra for candidate ranking and structure confirmation.

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26
26.Chem Thermochemistry

Compute gas-phase thermodynamic quantities (H, S, G) and reaction thermochemistry (ΔH, ΔS, ΔG) using MLIPs with the ideal-gas/rigid-rotor/harmonic-oscillator approximation.

learningmatter-mit/AtomisticSkills176—~1.4kAutomated safety check: PassMITtoday
27
27.Chem TS Optimization

Optimize non-periodic molecular TS guesses and verify first-order saddle point from vibrational modes.

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28
28.Chem Vibration

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

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29
29.Drug Bioactivity Assay

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

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30
30.Drug DB Chembl

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

learningmatter-mit/AtomisticSkills176—~1.4kAutomated safety check: PassMITtoday
31
31.Drug DB Pdb

Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.

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32
32.Drug DB Pubchem

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

learningmatter-mit/AtomisticSkills176—~1.3kAutomated safety check: PassMITtoday
33
33.Drug Docking Analysis

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

learningmatter-mit/AtomisticSkills176—~2.2kAutomated safety check: PassMITtoday
34
34.Drug Docking Vina

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

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35
35.Drug Ligand Prep

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

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36
36.Drug Mmpbsa Gbsa

Compute single-trajectory MM-GBSA and / or MM-PBSA binding free energy estimates from a protein-ligand MD trajectory.

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37
37.Drug Pose Validation

Validate docked or generated ligand poses for physical plausibility using PoseBusters, filtering out chemically invalid or clashing poses before downstream refinement.

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38
38.Drug Protein Ligand Md

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/AtomisticSkills176—~1.4kAutomated safety check: PassMITtoday
39
39.Drug Protein Prep

Prepare macromolecular receptor structures (PDB/mmCIF or RCSB PDB ID) for docking or simulation by fixing common structure issues and adding hydrogens.

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40
40.Drug Redocking Rmsd

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

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41
41.Drug Retrosynthesis

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

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42
42.Drug Trajectory Analysis

Analyze a protein-ligand MD trajectory to compute ligand RMSD, pocket RMSF, hydrogen bonds, contact occupancy, and protein-ligand interaction fingerprints over time.

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43
43.General Arxiv Search

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

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44
44.General Atomisticskills Setup

Set up, check or troubleshoot how AtomisticSkills runs on this machine -- creating its Python environments, connecting its MCP servers, choosing uv or a container runtime, and configuring API keys.

learningmatter-mit/AtomisticSkills176—~1.2kAutomated safety check: NotesMITtoday
45
45.General Biorxiv Search

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

learningmatter-mit/AtomisticSkills176—~854Automated safety check: PassMITtoday
46
46.General Chemical Literature

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

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47
47.General Chemical Pricing

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

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48
48.General Patent Search

Search for patents by keyword, material name, or assignee using free data sources (Google Patents).

learningmatter-mit/AtomisticSkills176—~540Automated safety check: PassMITtoday

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