Use when targeting Molecular Biology and Evolution (MBE) or deciding whether a molecular evolution manuscript fits this venue.
分子生物学设计与验证范畴路由。用于 PCR/qPCR 引物探针、CRISPR sgRNA pegRNA donor、限制性酶切和克隆图谱、质粒注释、RNA 二级结构和结构探针等实验设计任务，选择具体 skill 并生成可执行交接物。
Use when after a trained CNN model has generated molecular embeddings for query spectra, and you need to retrieve the most likely candidate molecules from a reference database.
Use when you have a curated dataset of small molecules with SMILES, optional 3D coordinates, adduct information, and experimentally measured CCS values (in Ångströms or similar…
Use when targeting Molecular Cell (Mol Cell) or deciding whether a molecular-biology manuscript fits this Cell Press venue.
Use when you have raw molecular structures in SMILES or SDF format and need to prepare molecular descriptors as input to a descriptor-based classifier (e.g., BitterPredic — from…
Use when you have SMILES strings or 2D molecular structures of N-Me derived unsaturated sterol lipids (or other C=C-containing molecules) and need to generate 3D conformational…
Use when you have 1D ¹H and/or ¹³C NMR spectra (as preprocessed numerical arrays or peak lists) from an unknown organic molecule with ≤19 heavy atoms, and you need to recover its…
Use when when setting up a ViMMS chemical sampling environment and you need to restrict the chemical search space to a specific m/z range (e.g., 100–1000) and MS level (e.g., MS1…
Use when you have raw molecular datasets (e.g., METLIN-CCS, CCSBase) with SMILES strings, 3D coordinates, adduct information, and ground-truth collision cross section labels, and…
Use when you have raw molecular structures in SMILES or SDF format and need to prepare them as input for BitterPredict.m or similar descriptor-based classifiers.
Use when when you have a query mass spectrum and a set of candidate molecular structures (as SMILES or 2D/3D coordinates), and you need to prepare them for cross-view similarity…
Use when when you have validated SMILES strings or canonical molecule objects from RDKit and need to convert them into the fixed-size numerical tensor format expected by a deep…
Use when you have a collection of chemical structures (SMILES, InChI, SDF, or mol formats) and need to train or apply a machine learning model for retention time prediction or…
OneScience 小分子生成与药物设计模型 skill。用于 MolSculptor 的 SMILES/分子图、autoencoder、latent diffusion、分子优化、reward、DSDP/docking 相关 case、训练和推理任务。
Use when after SMILES standardization when you have a table of translated SMILES strings (e.g., interim/tables/1_translated/structure/smiles.tsv.
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD,…
Use when targeting Molecular Ecology (Mol Ecol) or deciding whether a manuscript applying molecular approaches to ecological, evolutionary, or conservation questions fits this…
Use when you have downloaded and extracted a GNPS archive (from METABOLOMICS-SNETS,
Use when you have untargeted metabolomics peak intensity data and spectral groupings (Molecular Families or Mass2Motifs) but lack confident chemical annotations or want to avoid…
Use when you have loaded a collection of molecular fingerprint vectors (e.g., from biosynfoni fingerprints deposited in Zenodo) and need to assess their statistical properties…
Use when you have natural product molecules (or compounds from natural product-like databases such as COCONUT or ZINC) in structural format (SMILES, InChI, or SDF file) and need a…
Use when you have annotated metabolite structures (with SMILES strings) from a reference library (e.
Use when you have received a JSON response from the CSI:FingerID web service endpoint after submitting a fragmentation tree or tandem mass spectrum query, and you need to extract…
Use when when you have labeled mass-spectrometry spectral data (precursor m/z and fragment m/z–intensity pairs) paired with known molecular structures (as InChIKeys or SMILES),…
Use when when evaluating how well mass spectral similarity scores correlate with actual chemical structure for annotated spectral pairs (e.g., spectra with InChIKey metadata).
Use when you have a calibrated FT-ICR transient (ESI_NEG or similar ionization mode) and need to annotate each detected m/z peak with its most likely elemental composition.
Use when processing tandem MS/MS libraries in mgf format (such as GNPS) that lack a Molecular Formula (MF) field but contain valid SMILES strings.
Use when when you need to constrain a large metabolite database to a specific instrumental range (e.g., m/z 100–1000) before generating virtual chemical mixtures for LC-MS/MS…
Use when you have MS/MS fragmentation spectra (from Orbitrap or Q-TOF instruments) in MGF format with known precursor m/z, adduct type, and collision energy, and you need to…
Use when you need to represent, validate, and manipulate molecular compositions in MS analysis—specifically when annotating precursor or product ions with elemental formulas,…
Use when you have a recalibrated FT-ICR mass spectrum (Bruker .d format or equivalent) with detected, noise-thresholded peaks and need to assign chemical formulas to each peak.
Use when when you have a feature list from HRMS with tentatively assigned molecular formulas (from in silico tools or databases) and need to assess formula plausibility before…
Use when when you have encoded spectral features (from a CNN featurizer applied to 1D 1H and/or 13C NMR spectra) and a set of candidate molecular fragments predicted for a…
Use when after RDKit has generated multiple conformations for a molecule in an SDF or XYZ format, and you need to reduce the conformational ensemble to a tractable size (by…
Use when you have raw SMILES strings from a chemical database (e.g., CCSBase, METLIN, or custom sources) and need to feed them into a graph neural network model.
Use when when you have a collection of molecular structures (as InChI strings, SMILES, or RDKit Mol objects) and need to feed them into a pretrained or transfer-learning neural…
Use when you have molecular identifiers (SMILES strings or molecular structure files) that need to be converted into node-edge graph tensors for input to message passing neural…
Use when during MSP, MGF, JSON, or CSV file parsing when standardizing mass spectra from heterogeneous open mass spectral libraries (OMSLs).
Use when you have a GNPS mass spectral molecular network (classical or feature-based) and MS2LDA-derived Mass2Motif data, and you need to annotate network nodes with both chemical…
Use when you have a GNPS mass spectral molecular network (in .graphml or Cytoscape format) and wish to annotate its nodes and edges with chemical class assignments from the GNPS…
Use when after generating candidate transformed structures from biotransformation rules and when you have MS/MS spectral feature data that you wish to organize into putative…
Use when you have untargeted metabolomics data (e.g., LC-MS/MS spectra) and need to organize compounds by structural relatedness to enable structure discovery for unknown…
Use when you have a GNPS-generated classical or feature-based molecular network (in graphml or JSON format) and corresponding MS2LDA or chemical class assignment data, and you…
Use when after GNPS_GC molecular networking job completion, when you have retrieved raw network output files and need to extract, validate, and structure the network topology for…
Use when you have a GNPS-generated molecular network (classical or feature-based
Use when you have LC-MS/MS DDA data from one or more samples and need to organize fragmentation spectra by similarity relationships to support compound annotation, enable…
Use when targeting Molecular Psychiatry (Mol Psychiatry) or deciding whether a biological psychiatry or translational neuroscience manuscript fits this venue.
Generates academic reviews for molecules in diseases using PubMed research. Invoke when user needs biomedical literature review with Vancouver citation format.
Standardizes molecular structures using ChEMBL chembl_structure_pipeline and RDKit rdMolStandardize covering sanitization, salt/solvent stripping, neutralization, tautome — from…
Use when you have a trained GNN model predicting CCS values from molecular graphs and need to understand which structural features (node and edge attributes) are most influential…
Use when you have a collection of molecular structures (with SMILES strings, InChI, or similar identifiers) and corresponding experimentally determined or reference CCS values,…
Use when when you have a set of chemical structures (SMILES strings or SDF files) that need to be processed for training a graph neural network model on molecular property…
Use when after an end-to-end neural model (CNN + transformer) has generated predicted molecular structures (formula and connectivity) from 1D NMR spectra.
Use when you are receiving molecular structures from external sources (COCONUT database, ZINC database, user-provided chemical data) in varying formats (SMILES strings, InChI…
Use when you have trained a multitask NMR-to-structure model and need to quantify its predictive accuracy on held-out test molecules.
Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra (as numerical arrays or feature tensors) from an unknown organic compound with ≤19 heavy atoms, and you need to predict…
Use when your goal is to assess whether a pretrained NMR2Struct model trained on molecules ≤19 heavy atoms can generalize to larger, more complex molecules, or whether accuracy…
Use when when you have executed the MultiModalSpectralTransformer architecture on a set of multi-modal spectroscopic inputs (NMR, HSQC, COSY, IR) and obtained predicted molecular…
Use when when you have paired mass spectra and molecular structure data and need to train a model that can bidirectionally map between experimental spectra and chemical s — from…