'smiles' 검색 결과

Estimate small molecule solubility, permeability, and lipophilicity with Boltz using SMILES, a text notation for molecular structures. Process individual molecules or lists, review costs before submission, and receive results mapped to each input.

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• Estimate properties for a molecule from its SMILES
• Evaluate a molecule list from a CSV file
• Compare predicted properties during initial screening

Process molecular datasets in Python through a simpler interface to RDKit, a chemistry toolkit. Convert and standardize structures, calculate molecular properties, compare and cluster compounds, generate 3D conformations, and visualize results for drug discovery workflows.

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• Load and standardize molecular datasets
• Calculate molecular properties and similarities
• Cluster compounds and select diverse subsets

Generate candidate positions and orientations for small molecules binding to proteins with DiffDock and DiffDock-L. Prepare single or batch docking runs, organize predicted poses by model confidence, and review validation needs without treating confidence as binding affinity.

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• Predicting binding poses for a protein and small molecule
• Preparing and validating batch docking inputs
• Comparing poses across receptor conformations

Screen an existing compound library against a protein target with Boltz. Rank candidates by binding confidence or lead optimization score, download predicted structures, and review solubility, permeability, and lipophilicity results alongside the ranked hits.

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• Screening an existing compound library against a protein
• Finding candidates with high binding confidence
• Comparing candidates for lead optimization

Read, analyze, modify, and visualize molecular structures with RDKit in Python. Calculate molecular properties, search for similar structures or specific structural patterns, apply reaction rules, and generate 2D or 3D coordinates with detailed control over processing.

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• Calculating properties for a collection of molecules
• Searching for molecules with similar structures
• Filtering molecules by specific structural patterns

Turn small-molecule structures into numerical features for similarity searches and models that predict activity or properties. Using Molfeat, the skill covers representation choices, invalid inputs, alignment with experimental labels, and saving feature-generation settings for reuse.

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• Prepare molecular features for activity or property prediction
• Choose molecular representations for similarity searches
• Keep experimental labels aligned after rejecting invalid molecules

Build molecular property prediction workflows with DeepChem for solubility, toxicity, and related chemistry tasks. Prepare molecular representations, choose compatible models, handle missing labels, and evaluate predictions using data splits designed for the intended scientific question.

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• Predicting solubility from molecular structures
• Comparing graph models on MoleculeNet datasets
• Checking data splits for information leakage

Look up compound–target binding data in BindingDB using PDB or UniProt identifiers, or search for similar chemical structures. Receive concise summaries of matching records, with full API responses saved to a file when requested.

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• Find ligands linked to a PDB identifier
• Look up binding data for a UniProt entry
• Search for compounds with similar structures

Strict SMILES validation, structural comparison, and modification verification. Catches invalid LLM-generated molecules.

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Train and run Uni-Mol Tools models to predict molecular properties from CSV data. Organize experiments into projects, compare model performance, rank results, and manage storage through interactive commands or machine-readable JSON output.

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• Train molecular property models from CSV data
• Predict properties with a trained model
• Organize experiments and compare model performance

Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration, motif extension, lead optimization, SAFE notation, QED or LogP ranking, hosted NVIDIA API calls, or local Docker deployment. GenMol takes SAFE notation in the smiles field, not ordinary SMILES.

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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.

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Cheminformatics toolkit for fine-grained molecular control. Parse and write SMILES, SDF, MOL and InChI; compute descriptors (MW, LogP, TPSA, QED, Bertz); build fingerprints (Morgan/ECFP, RDKit, MACCS, atom pair, torsion) and score Tanimoto, Dice or cosine similarity; run SMARTS substructure search and reaction SMARTS; generate 2D depictions and ETKDG 3D conformers; extract Murcko scaffolds and canonical hashes; control sanitization and stereochemistry directly. Also trigger on rdkit, Chem.MolFromSmiles, rdFingerprintGenerator, SDMolSupplier, SMARTS query, ETKDG, or FilterCatalog. For standard workflows with a simpler interface use the datamol skill, which wraps RDKit; use rdkit for advanced control, custom sanitization, and specialized algorithms.

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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.

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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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Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including 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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Screen compound libraries for drug discovery using drug-likeness guidelines, structural alerts that flag patterns for review, and molecular complexity measures. Combine criteria to shortlist candidates and retain filtering results with reasons for further assessment.

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• Screen compound libraries with drug-likeness rules
• Flag PAINS and other structures for review
• Combine property, structure, and complexity filters

Create original SVG illustrations with expressive cartoon characters, bold ink outlines, and a prominent prop. Use the transparent artwork for onboarding, empty states, success screens, blog headers, or marketing cards, with checks for consistent styling and believable hands.

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• Illustrations for onboarding screens
• Character artwork for empty states and error pages
• Celebratory illustrations for success screens

Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified residues. FoldBench Ab-Ag 50-55%, PPI 70-77% DockQ-pass. Also covers the ESMC-{300M,600M,6B} protein language models from the same release: masked-LM logits, hidden states, mutation scoring, contact prediction, and the SAE interpretability head. MIT-licensed weights on HuggingFace org `biohub`. Use this skill when: (1) Predicting complex structures with single-sequence input, (2) Validating designed binders with ESMFold2-Fast, (3) Running ESMFold2 with MSA input, (4) Getting ESMC embeddings or per-residue mutation scores, (5) Choosing kernel backend and sampling-step settings for paper-faithful throughput.

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Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.

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Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source AlphaFold3 alternative with optional binding-affinity prediction.

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Core cheminformatics toolkit for SMILES/SDF/InChI parsing, descriptors (MW, LogP, TPSA), fingerprints, ECFP/Morgan fingerprints, substructure search, 2D/3D generation, similarity, reactions, and datamol-style molecule standardization when no separate wrapper skill is routed.

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Continue KERMT pretraining on a custom SMILES corpus with a grover_base, cmim, or hybrid checkpoint. Use a local checkpoint or optionally download a pinned Hugging Face model bundle using HF_TOKEN if configured. Run containerized training and write model bundles, prepared data, logs, and checkpoints to user-selected host directories.

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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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