57 件 ・ 関連度順
概要と使いどころ
Use Boltz2 NIM for biomolecular structure prediction and binding affinity. Invoke for Boltz2, protein structures, protein-ligand/DNA/RNA complexes, SMILES or CCD ligands, pIC50/IC50 affinity scoring, mmCIF output, hosted NVIDIA API calls, or local Docker deployment.
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Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
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Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.
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Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.
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离线批量解析、标准化、去盐、提取 parent、检查异常并按原始/标准化/parent 结构分组。用于清洗 SMILES、CSV、SDF、MolBlock，检查价态/立体化学/混合物，或为描述符、相似性检索和建模准备结构数据。
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整理和审查结构化化学反应，保留原始记录并检查参与物、角色、产率、重复、守恒和 ORD 合同。用于清洗 reaction SMILES、ORD 或反应表格。
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保守解析化学名称、SMILES、InChI、InChIKey、PubChem CID、ChEMBL ID 或 CAS RN，保留多源证据、相关形式、歧义和冲突。用于确认化学记录是谁、对齐开放数据库，或在结构标准化前选择候选。
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Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
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Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
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Use ONLY when the user asks to check, validate, review or audit analysis code for scientific correctness, or when you are the reviewer agent running its checks. Never run it unprompted as part of ordinary analysis work. Covers physics, earth/geo, biology, chemistry, social science and bioprocess/fermentation. Runs a deterministic domain-correctness gate that catches code which runs but is scientifically wrong (unit/dimension mismatch, Euclidean distance on lat/lon without a CRS, 0-based/1-based coordinate and strand errors, impossible SMILES valence, uncorrected multiple comparisons, averaging a categorical code, unconstrained kinetic-parameter fits, kLa computed from raw DO instead of the driving force, arithmetic mean of raw CFU counts, ANOVA/Tukey with no assumption check, a curvature DOE design fit with a first-order model, an ML model fit across process scales with no correction). Surfaces structured findings; never claims the code is correct.
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Reads, writes, and converts molecular file formats (SMILES, InChI, SDF V2000/V3000, MOL2, PDB, and BinaryCIF) using RDKit and Open Babel with rigorous handling of aromaticity perception, stereochemistry, implicit/explicit hydrogens, kekulization, and salt/fragment separation. Use when loading chemical libraries, debugging parse failures, or preparing molecules for downstream standardization, descriptor calculation, or docking.
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分子格式转换工具。支持在 .smi、.mol、.xyz、.gjf、.sdf 等格式之间转换，并可从 SMILES 或 2D 结构生成带坐标的 3D 结构。 当用户提到分子格式转换、3D构象生成、openbabel等需求时使用此skill。
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Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
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Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
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Diffusion-based docking that predicts protein-ligand poses without a predefined site. Use for blind docking, when traditional docking fails, or exploring multiple binding modes. Pipeline: prep protein (PDB) and ligand (SMILES/SDF), run inference, analyze confidence-ranked poses.
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Query the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look up substances by ZINC ID, resolve a SMILES to its ZINC ID (exact match), inspect purchasability/catalogs, and assemble compound sets for docking. Property (MW/logP) filtering is done locally with RDKit. For bioactivity use chembl-database-bioactivity; for approved drugs use drugbank-database-access.
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Cheminformatics toolkit for molecular analysis and virtual screening: SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints (Morgan/ECFP, MACCS), Tanimoto similarity, SMARTS substructure filtering, Lipinski drug-likeness, reaction enumeration, 2D/3D coordinates. For simpler API use datamol; use RDKit for fine-grained sanitization, custom fingerprints, or SMARTS/reaction control.
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Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required. Search by name/CID/SMILES/InChIKey/formula, retrieve properties (MW, XLogP, TPSA, H-bond counts), do similarity/substructure searches with async ListKey polling, fetch synonyms, descriptions, assay summaries, and download SDF/PNG. For local cheminformatics use rdkit; for bioactivity-centric workflows use chembl-database-bioactivity.
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Molecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit 2D, Mordred), pretrained embeddings (ChemBERTa, GIN, Graphormer), pharmacophores. Scikit-learn compatible with parallelization/caching. For QSAR, virtual screening, similarity, and molecular DL.
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Query IUPHAR/BPS Guide to Pharmacology (GtoPdb) for receptor-ligand interactions, target/ligand metadata, families, and approved drugs. Affinities (pKi/pIC50/pKd), action (Agonist/Antagonist/etc.), species, structures (SMILES/InChI). No auth. Always resolve targets via geneSymbol/accession; most metadata lives in sub-resources (/databaseLinks, /structure, /synonyms).
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Pythonic RDKit wrapper with sensible defaults for drug discovery. SMILES parsing, standardization, descriptors, fingerprints, similarity, clustering, diversity selection, scaffold analysis, BRICS/RECAP fragmentation, 3D conformers, and visualization. Returns native rdkit.Chem.Mol. Prefer datamol for standard workflows; use RDKit directly for advanced control.
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Parse local DrugBank XML for drug info, interactions, targets, and properties. Search by ID/name/CAS, extract DDIs with severity, map targets/enzymes/transporters, compute SMILES similarity. Primary via local XML; REST API rate-limited (3k/month dev). For live bioactivity use chembl-database-bioactivity; for compound properties use pubchem-compound-search.
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Filter rows of a Datagrok DataFrame via the datagrok_exec tool through the Filters panel — by range, equals/contains/in-set, multi-value, boolean, free-text row expressions, or substructure (SMILES / SMARTS / molblock). Also covers clearing, inverting, the show-only-filtered vs destructive-drop split, and the filter event lifecycle (onRowsFiltering / onFilterChanged / onRowsFiltered). Use whenever the user says "filter", "show only", "hide rows where", "narrow to subset", "find rows that", "contains", "substructure search", "categorical filter", "range filter", "invert", "clear the filter", "clear filters", "drop rows", or asks for the filtered subset as a new table. Does NOT cover selection (separate skill) or generic DataFrame cloning (datagrok-df-and-columns).
日本語の概要は準備中です。原文の説明を表示しています。
Molecular featurization hub with one consistent interface over 100+ featurizers. Fingerprints (ECFP/Morgan, MACCS, atom pair, topological torsion, Avalon, RDKit, ERG), RDKit and Mordred descriptor sets, pharmacophore and 3D shape descriptors, scaffold keys, and pretrained embeddings (ChemBERTa, ChemGPT, MolT5, GIN, Graphormer) through a common transformer API with caching and parallelism. Use this skill to convert SMILES into model-ready feature matrices for QSAR, virtual screening, and molecular ML, and to choose between featurizer families. Also trigger on molfeat, MoleculeTransformer, FPVecTransformer, PretrainedHFTransformer, molfeat model store, or featurizer selection.
日本語の概要は準備中です。原文の説明を表示しています。