71건 · 관련도순
Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by drug-likeness criteria.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
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.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating products from synthetic routes.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
对已标准化化合物确定性计算受控二维描述符、Morgan/RDKit/MACCS 指纹和数据集质量画像。用于准备分子特征、生成指纹，或检查特征缺失、常数、异常和分布。
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Enumerates virtual chemical libraries via reaction SMARTS transformations using RDKit and reaction templates, with explicit handling of atom mapping, RDChiral template extraction, product validation, RECAP/BRICS fragmentation, R-group decomposition, matched molecular pair analysis (MMPA), and Free-Wilson analysis. Use when generating combinatorial libraries from building blocks, enumerating analog series, deriving structure-activity rules, or extracting transformations from reaction data.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Builds and applies 3D pharmacophore models using RDKit Pharm3D, the apo2ph4 receptor-based workflow (Heider et al. 2023), Pharmer / Pharmit for search, and PharmacoForge for protein-pocket-conditioned pharmacophore generation (Flynn et al. 2025), covering ligand-based pharmacophores from active-set alignment and receptor-based pharmacophores from binding-pocket geometry. Explicitly handles feature types, geometric tolerances, partial matching, and pharmacophore-based virtual screening. Use when identifying scaffold-hopping candidates, building shape-and-feature search queries, or transferring SAR across chemotypes.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
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.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Calculates molecular fingerprints (ECFP/Morgan, FCFP, MACCS, RDKit, AtomPair, TopologicalTorsion, Avalon, MAP4, MHFP6) and physicochemical descriptors (Lipinski, QED, TPSA, Crippen LogP, 3D shape) with explicit choice tables, bit vs count semantics, and partial-charge model selection. Use when featurizing molecules for similarity, QSAR, virtual screening, or ML, or selecting the correct fingerprint for a chemotype-aware task.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Molecular docking with AutoDock Vina (Python API). Receptor/ligand prep (Meeko + RDKit), grid box, docking, pose and binding energy analysis, and batch virtual screening.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
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.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (--custom_scoring), local optimization of an existing pose (--local_only), per-atom contributions (--atom_term_data), or SDF/MOL2 ligands without manual PDBQT conversion. For unknown binding sites use diffdock; for the Python-bindings/Vinardo workflow use autodock-vina-docking.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
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.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
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.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Deep learning for drug discovery. 60+ models (GCN, GAT, AttentiveFP, MPNN, ChemBERTa, GROVER), 50+ featurizers, MoleculeNet benchmarks, HPO, transfer learning. Unified load-featurize-split-train-evaluate API. For fingerprints use rdkit-cheminformatics; for featurization-only use molfeat.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. Monte Carlo tree search guided by a template-based neural expansion policy recursively disconnects a target SMILES until precursors are found in a purchasable stock. Covers config.yml (v4 format), aizynthcli batch screening, the AiZynthFinder/AiZynthExpander Python API, one-step disconnections, custom stocks via smiles2stock, scorers, Retro*/breadth-first/DFPN search alternatives, and reading output.json.gz / trees.json. Use for synthesis route planning, synthesizability screening, and building-block/precursor search. For reaction barriers use neb-irc-activation-energy; for 2D reaction scheme drawing use rdkit-chemdraw-cdxml.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
NEB-IRC activation energy pipeline for reaction barriers using GFN2-xTB and pysisyphus. Optimize reactant and product geometries, run CI-NEB path search, optimize the transition state with a Hessian, verify with IRC (one imaginary mode, endpoints matching reactant/product, single NEB maximum), and report the electronic and Gibbs barriers. Use when you need a transition state, reaction barrier, activation energy, minimum energy path, or intrinsic reaction coordinate. Covers reactant/product atom-ordering pitfalls, feasibility sizing for single-core runs, and thermochemistry corrections. Renders an IRC energy-profile plot and an animated TS imaginary-mode HTML viewer. For 2D reaction scheme drawing use rdkit-chemdraw-cdxml.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, MD or reaction-path playback, docking poses, and orbital/density isosurfaces. For static 2D chemical structure drawings use rdkit-chemdraw-cdxml; for 2D statistical plots use matplotlib or plotly.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Protein language models (ESM3, ESM C) for sequence generation, structure prediction, inverse folding, and embeddings. Design novel proteins, extract ML features, or fold sequences. Local GPU or EvolutionaryScale Forge API. Use AlphaFold for traditional folding; RDKit for small molecules.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Guides agents using the datamol Python package for RDKit-first molecular IO, preparation, fingerprints, similarity, structure generation, visualization, and utility workflows.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Think and work like an expert Cheminformatician. Use when a task calls for Cheminformatician judgment. Reasons from Standard InChI identity and RDKit sanitization through ChEMBL pChEMBL harmonization, Morgan/ECFP fingerprints, scaffold splits and applicability domains, while treating tautomer collapse, KNIME-vs-Python canonicalization drift, and random-split QSAR leakage as first-class failure modes.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Cheminformatics toolkit catalog for small molecules. Covers RDKit/OpenChemLib calculations, descriptors, fingerprints, similarity/substructure search, R-group, MMP, scaffold tree, chemical space, MPO, reactions, and ADMET predictions. Open this skill when the user asks about computing molecular properties, comparing/searching molecules, or predicting ADMET/tox.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.