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deepchem
【数据与研究】Builds molecular property prediction and MoleculeNet workflows with DeepChem, including SMILES featurization, scaffold or grouped holdouts, masked labels, graph models and explicit pretrained encoder transfer. Used for ADMET, toxicity, solubility and chemistry ML when DeepChem data/model contracts and scientific validation are needed.
hugging-science
【设计与创意】Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting scientific ML resources in biology, chemistry, genomics, materials, climate, physics, astronomy, medicine, mathematics, protein design, single-cell analysis, or PDE modeling, and when checking their actual datase…
marine-carbonate-chemistry
【数据与研究】Solves seawater carbonate chemistry with PyCO2SYS for chemical oceanography, ocean acidification, and marine carbon-cycle research. Use for paired total alkalinity, dissolved inorganic carbon, pH, or seawater pCO2/fCO2 measurements; carbonate speciation; aragonite and calcite saturation; Revelle factors; lab-to-in-situ temperature and pressure correc…
medchem
【效率与协作】Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.
rowan
【效率与协作】Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling ta…
medchem
【效率与协作】Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.
green-chemistry-metrics
【开发与工程】Green chemistry metrics calculation skill for atom economy, E-factor, and process mass intensity
ligand-exchange-protocol-manager
【开发与工程】Surface chemistry skill for managing ligand exchange reactions, bioconjugation protocols, and functional group quantification
pyscf-quantum-chemistry
【开发与工程】PySCF quantum chemistry skill for molecular calculations, coupled cluster, and multireference methods
pyscf-interface
【效率与协作】PySCF quantum chemistry interface for classical electronic structure calculations
qiskit-nature-solver
【数据与研究】Qiskit Nature skill for quantum chemistry and materials science applications
tooluniverse-chemical-compound-retrieval
【数据与研究】Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing), fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity…
tooluniverse-inorganic-physical-chemistry
【数据与研究】Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, lattice parameters, thermodynamic properties, electronic structure. Use for unit cell volume calculations, coordination geometry, materials property estimation, and inorganic-mechanism reasoning. Complementary to tooluniverse-organic-chemistry.
tooluniverse-organic-chemistry
【数据与研究】Organic chemistry reasoning guide for reaction product prediction, mechanism analysis (electrophilic/nucleophilic substitution, addition, elimination, pericyclic, radical), and spectroscopy interpretation (1H/13C NMR, IR, MS). Reasons from first principles (electron flow, kinetic vs thermodynamic) rather than pattern-matching named reactions. Use for…
tooluniverse-chemical-compound-retrieval
【数据与研究】Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing), fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity…
tooluniverse-inorganic-physical-chemistry
【数据与研究】Inorganic chemistry, physical chemistry, and materials science — crystal structures, coordination chemistry, lattice parameters, thermodynamic properties, electronic structure. Use for unit cell volume calculations, coordination geometry, materials property estimation, and inorganic-mechanism reasoning. Complementary to tooluniverse-organic-chemistry.
tooluniverse-organic-chemistry
【数据与研究】Organic chemistry reasoning guide for reaction product prediction, mechanism analysis (electrophilic/nucleophilic substitution, addition, elimination, pericyclic, radical), and spectroscopy interpretation (1H/13C NMR, IR, MS). Reasons from first principles (electron flow, kinetic vs thermodynamic) rather than pattern-matching named reactions. Use for…
bio-single-cell-splicing
【数据与研究】Analyzes alternative splicing at single-cell resolution. The first decision is library chemistry — 10X 3' is fundamentally limited (RT primes from poly-A, R2 falls in 3' UTR, <0.1 junction read per cell per AS event). Plate-based full-length methods (Smart-seq3, FLASH-seq, VASA-seq, STORM-seq) and single-cell long-read (MAS-Iso-seq, scISOr-Seq2) are …