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Scientific tool catalog

Every scientific catalog entry, with a purpose, documentation link, and setup or availability details.

This version lists 54 scientific capabilities. The catalog includes supported local setup paths, connected scientific tools, reference entries, and unavailable entries. These are different levels of support; the list is not a count of ready-to-run tools.

Start with availability

Open Customize → Tools and search the name. Check readiness, follow a supported setup or connection action, and validate a small known input before a larger run. The supported integrations remain experimental in this catalog; inspect the current app status and output checks.

Try: "Check whether RDKit is ready. If it is, validate the SMILES in data/molecules.csv and save molecular weights, invalid records, and the script in the project."

For reference entries, the source link explains the underlying software. Use a separately configured environment or an appropriate skill if you choose to work with it; a reference entry alone does not make it available to the agent.

Find a tool

Analysis

Cantera

Chemical kinetics, thermodynamics, and transport simulations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: cantera

ChemPy

Chemical-reaction, equilibrium, kinetics, and formula calculations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: chempy

lmfit-py

Nonlinear least-squares minimization and curve fitting.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: lmfit

nmrglue

Reading, processing, and converting NMR spectroscopy data.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: nmrglue

PyAlex

Analysis tooling represented by the audited PyPI project.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: pyalex

pybaselines

Baseline correction algorithms for experimental signals.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: pybaselines

scikit-learn

Classical machine-learning models, preprocessing, model selection, and metrics in Python.

How to use: Check readiness in Tools, follow setup, and request a small validated calculation. Setup guide.

Documentation and source · Catalog identifier: scikit-learn

SciPy

Numerical optimization, integration, signal processing, and scientific statistics in Python.

How to use: Check readiness in Tools, follow setup, and request a small validated calculation. Setup guide.

Documentation and source · Catalog identifier: scipy

statsmodels

Statistical models, tests, and econometric analysis in Python.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: statsmodels

thermo

Chemical engineering thermodynamics and property calculations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: thermo

Bioinformatics

Biopython

Sequence, alignment, structure-file, and common bioinformatics data handling in Python.

How to use: Check readiness in Tools, follow setup, and request a small validated calculation. Setup guide.

Documentation and source · Catalog identifier: biopython

ESM-2

Protein language-model embeddings and sequence representations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: esm-2

multiple-sequence-alignment search.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: msa-search

Cheminformatics

Chemprop

Message-passing neural networks for molecular property prediction.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: chemprop

DeepChem

Machine-learning components for molecular and materials workflows.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: deepchem

GenMol

molecular generation.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: genmol

molmass

Molecular-mass and elemental-composition calculations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: molmass

MolMIM

molecule generation and optimization.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: molmim

Mordred

Molecular descriptor calculation.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: mordred

Open Babel

Chemical file conversion, filtering, and molecular operations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: open-babel

PubChemPy

Python client access to PubChem records and searches.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: pubchempy

RDKit

Molecular parsing, descriptors, fingerprints, conformers, and cheminformatics workflows.

How to use: Check readiness in Tools, follow setup, and request a small validated calculation. Setup guide.

Documentation and source · Catalog identifier: rdkit

Chromatography

hplc-py

HPLC chromatogram baseline correction, peak fitting, and quantification.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: hplc-py

Docking

AutoDock Vina

Molecular docking and virtual-screening command-line workflows.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: autodock-vina

DiffDock

protein-ligand pose generation.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: diffdock

Document

chemdataextractor2

Chemical information extraction from scientific text.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: chemdataextractor2

Marker

Document conversion to structured Markdown and related formats.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: marker

paper-qa

Question answering and evidence synthesis over scientific papers.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: paper-qa

Genomics

Evo 2

DNA sequence generation.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: evo2

Mass spectrometry

matchms

Mass-spectrum import, filtering, similarity, and matching.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: matchms

OpenMS

Proteomics and metabolomics mass-spectrometry processing.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: openms

Pyteomics

Proteomics and mass-spectrometry data parsing and calculations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: pyteomics

Molecular modeling

OpenMM

Molecular simulation with CPU and GPU backends.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: openmm

pymatgen

Materials structures, transformations, and analysis.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: pymatgen

Protein design

ProteinMPNN

structure-conditioned protein sequence design.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: proteinmpnn

RFdiffusion

protein backbone generation.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: rfdiffusion

Quantum

cclib

Parsing and analysis of computational-chemistry log files.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: cclib

CREST

Conformer-rotamer ensemble sampling around the xtb electronic-structure engine.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: crest

GoodVibes

Thermochemical corrections and analysis for quantum-chemistry outputs.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: goodvibes

NWChem

Large-scale computational chemistry workflows.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: nwchem

Psi4

Open-source quantum chemistry calculations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: psi4

PySCF

Python-based quantum-chemistry calculations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: pyscf

xtb

Semiempirical extended tight-binding calculations.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: xtb

Structure

AlphaFold2

Protein structure prediction requiring reviewed weights, databases, storage, licensing, and a GPU runtime.

How to use: Unavailable in this catalog. Review prerequisites in the linked source; choose another supported tool.

Documentation and source · Catalog identifier: alphafold2

AlphaFold2-Multimer

Multimeric protein structure prediction with AlphaFold model weights and databases.

How to use: Unavailable in this catalog. Review prerequisites in the linked source; choose another supported tool.

Documentation and source · Catalog identifier: alphafold2-multimer

Boltz-2

biomolecular structure and affinity prediction.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: boltz2

cctbx_project

Computational crystallography libraries and command-line programs.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: cctbx-project

ESMFold

Protein structure prediction using ESMFold model weights.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: esmfold

Gemmi

Crystallographic structure and reflection data handling.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: gemmi

OpenFold2

monomer structure prediction from MSA and templates.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: openfold2

OpenFold3

multimolecule structure prediction.

How to use: An NVIDIA BioNeMo NIM. Connect your NVIDIA API key, check accepted inputs and cost, then try a small case. Connection guide · BioNeMo Agent Toolkit.

Documentation and source · Catalog identifier: openfold3

Synthesis

AiZynthFinder

Retrosynthetic route planning.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: aizynthfinder

Syntheseus

Retrosynthesis algorithm benchmarking and route search.

How to use: Reference entry: this release does not install or execute it through Tools. Follow the linked source for your own setup and use compatible skills or scripts.

Documentation and source · Catalog identifier: syntheseus

Visualization

Matplotlib

Static scientific plotting and publication-oriented figure generation in Python.

How to use: Check readiness in Tools, follow setup, and request a small validated calculation. Setup guide.

Documentation and source · Catalog identifier: matplotlib

Use Built-in research tools for file operations, Python, R, search, and jobs. Use Scientific databases for records, Scientific viewers to inspect data, and the Skill directory for research procedures.

Edit this page Documentation index