122건 · 관련도순
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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Use the fair-esm repository skill for protein language-model embeddings, ESMFold structure prediction, ESM-IF1 inverse folding, and zero-shot variant-effect scoring.
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Use ColabFold for protein structure prediction workflows: validate FASTA/CSV/A3M inputs, generate MSAs, plan batch predictions, inspect outputs, and troubleshoot optional AlphaFold, MMseqs2, JAX, GPU, and OpenMM dependencies.
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Guide alphafold2-pytorch protein sequence, MSA, distogram, angle-logit, coordinate-refinement, recycling, embedding, and structure-utility workflows with version-aware troubleshooting.
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Route AlphaFold protein structure prediction setup, data preparation, local prediction, model configuration, output interpretation, and relaxation workflows.
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Use AlphaFold 3 PyTorch for protein and biomolecular structure-prediction workflows, heterogeneous molecule inputs, PDB/mmCIF/MSA/template preparation, bounded model inference, training configuration, and local CLI or Gradio operation.
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Think and work like an expert Animal Nutritionist. Use when a task calls for Animal Nutritionist judgment. Reasons from NASEM/AAFCO requirements, SID amino acids and ideal protein, CNCPS MP/NE balance, and NANP feed libraries through NIR-wet chemistry validation, ileal vs fecal digestibility, pen-structured mixed models, and ARRIVE reporting while treating intake confounds, NIR calibration drift, acidosis/sorting, and pseudoreplicated pens as first-class failure modes.
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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.
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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.
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Carbon chemistry, functional groups, IUPAC nomenclature, isomerism, reaction mechanisms (substitution, elimination, addition), polymers, and biochemistry basics. Covers hydrocarbon classes (alkanes, alkenes, alkynes, aromatics), common functional groups (alcohols, aldehydes, ketones, carboxylic acids, esters, amines, amides), stereochemistry, condensation and addition polymerization, and the four biomolecule classes (carbohydrates, lipids, proteins, nucleic acids). Use when analyzing organic structures, predicting reaction products, or connecting chemistry to biology.
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Turn a set of structures into absorption, distribution, metabolism, excretion, and toxicity estimates with ADMET-AI, and read them as a developability verdict rather than a table of numbers. Use this skill to run batch prediction over a library, interpret each endpoint against its DrugBank-approved percentile, and flag the liabilities that stop a series — hERG blockade, CYP inhibition, poor Caco-2 permeability, high clearance, and plasma protein binding. Also trigger on ADMET-AI, admet_ai, Chemprop-RDKit, hERG liability, CYP3A4 inhibition, Caco-2, bioavailability prediction, or developability triage.
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Work on bifunctional degraders and molecular glues, where potency comes from a ternary complex rather than occupancy. Use this skill to apply the property rules that govern this beyond-rule-of-five space, reason about linker length, attachment vector and E3 ligase choice, prepare inputs for ternary complex structure prediction, and interpret degradation readouts — DC50, Dmax, cooperativity, and the hook effect that makes a dose-response curve turn over. Also trigger on PROTAC, molecular glue, targeted protein degradation, E3 ligase, cereblon, VHL, ternary complex, DC50, Dmax, hook effect, cooperativity, or PROTAC-DB.
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Query the ChEMBL database web services for measured bioactivity data, compound records and calculated properties, targets, assays, mechanisms of action, drug indications and warnings. Use this skill to build curated SAR or QSAR datasets for a target, look compounds up by SMILES, InChIKey, name, or ChEMBL id, run similarity and substructure searches, and check what chemistry is already known against a protein. Also trigger when a query mentions ChEMBL ids (CHEMBL...), pChEMBL values, IC50/Ki/Kd/EC50 retrieval, assay confidence scores, or ebi.ac.uk/chembl.
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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.
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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.
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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.
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Publication-quality molecular visualization. 2D structure drawings (PNG/SVG), molecule grids with property annotations, scaffold highlighting, protein-ligand interaction diagrams, and interactive 3D views.
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Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.
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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Performs structure-based virtual screening using AutoDock Vina, SMINA, GNINA (CNN scoring), and DiffDock-L hybrid workflows with explicit choice rules across rigid vs flexible docking, cross-docking vs self-docking, binding-site detection (P2Rank, fpocket), receptor preparation (PDB2PQR, PROPKA), ligand preparation (meeko, OpenBabel), and ultralarge-library screening (ZINC22, Enamine REAL). Use when screening chemical libraries against a protein target to find candidate binders, ranking docking poses, or selecting a docking workflow for a specific scenario.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.
Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.
한국어 요약은 준비 중입니다. 원문 설명을 표시하고 있습니다.