115 skills · sorted by relevance
Create automated workflows that add threat intelligence to suspicious IP addresses, domains, URLs, and file hashes. Combine findings from multiple services into consistent alert context and confidence scores to support analysts reviewing security alerts.
Design amino acid sequences from a protein backbone using SolubleMPNN, a model trained on soluble protein structures. Generate candidates with a solubility bias for redesigning aggregation-prone proteins or preparing an E. coli expression screen.
Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.
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Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).
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Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.
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Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.
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跨版本符号迁移与二进制差分。当你有旧版本的符号/逆向结果，需要快速迁移到新版本时使用。 适用场景：内核缺 PDB 用旧版符号推导、程序更新后批量迁移函数名、应用更新后快速定位新偏移。 核心方法：用 LLM 做结构化差异比对，程序化输入输出，成本极低（200 函数 ~1 元）。 触发关键词：符号迁移、bindiff、跨版本、PDB 缺失、函数偏移迁移、symbol migration、binary diff、版本对比。
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Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth. For atomic coordinates use pdb-database; for AlphaFold predictions use alphafold-database-access.
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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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Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
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Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search entries, retrieve a protein's domains, list family members, get taxonomic distribution, link to PDB. Unifies Pfam, PANTHER, PIRSF, PRINTS, PROSITE, SMART, CDD, NCBIfam. Use uniprot-protein-database for sequences; pdb-database for 3D structures.
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Molecular biology toolkit: sequence manipulation, FASTA/GenBank/PDB I/O, NCBI Entrez, BLAST automation, pairwise/MSA alignment, Bio.PDB, phylogenetic trees. Use for batch processing, custom pipelines, format conversion, PubMed/GenBank queries. For quick gene lookups use gget; for multi-service REST APIs use bioservices.
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Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures. For structure retrieval, use pdb. For sequence design, use proteinmpnn.
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跨版本符号迁移与二进制差分。当你有旧版本的符号/逆向结果，需要快速迁移到新版本时使用。 适用场景：内核缺 PDB 用旧版符号推导、程序更新后批量迁移函数名、游戏反作弊更新后快速定位新偏移。 核心方法：用 LLM 做结构化差异比对，程序化输入输出，成本极低（200 函数 ~1 元）。 触发关键词：符号迁移、bindiff、跨版本、PDB 缺失、函数偏移迁移、symbol migration、binary diff、版本对比。
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Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native contacts, PCA and free energy surfaces. Use this skill for protein stability under mutation, ligand binding-mode and residence-time questions, conformational sampling, membrane proteins, and disordered ensembles. Also trigger on OpenMM, MDAnalysis, mdtraj, Simulation.step, LangevinMiddleIntegrator, PDBFixer, DCD or XTC trajectory, RMSD analysis, or production MD.
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Structure-based docking with AutoDock Vina, Vinardo, and AutoDock4 through the Meeko toolchain. Use this skill to define a docking box, prepare receptors and ligands as PDBQT, run single or batch docking, rescore, and interpret affinities, poses, and ligand efficiency. Covers box definition from a reference ligand or pocket residues, protonation and tautomer decisions, flexible side chains, exhaustiveness and seeds, redocking validation, and virtual screening over compound libraries. Also trigger on vina, smina, gnina, mk_prepare_ligand, mk_prepare_receptor, mk_export, scrub.py, PDBQT, autogrid4, docking box, or binding-pose prediction.
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AbuseIPDB API reference. IP reputation and abuse report lookups.
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Improves GKE workload reliability, using PDBs, health probes, and topology spread constraints. Use when configuring GKE workload reliability, setting up PDBs, or configuring GKE health probes (liveness, readiness, startup). Don't use for disaster recovery setup or full cluster backups (use gke-backup-dr instead).
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Patterns for controlling interactive debuggers (pdb, ipdb, gdb, lldb, node debug) via terminalcp
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Automate Abuselpdb tasks via Rube MCP (Composio). Always search tools first for current schemas.
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Automate Abuselpdb tasks via Rube MCP (Composio). Always search tools first for current schemas.
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Analyzes indicators of compromise (IOCs) including IP addresses, domains, file hashes, URLs, and email artifacts to determine maliciousness confidence, campaign attribution, and blocking priority. Use when triaging IOCs from phishing emails, security alerts, or external threat feeds; enriching raw IOCs with multi-source intelligence; or making block/monitor/whitelist decisions. Activates for requests involving VirusTotal, AbuseIPDB, MalwareBazaar, MISP, or IOC enrichment pipelines.
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Automate Abuselpdb tasks via Rube MCP (Composio). Always search tools first for current schemas.
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Access AlphaFold DB's 200M+ predicted structures by UniProt ID. Download PDB/mmCIF, analyze pLDDT/PAE, bulk-fetch proteomes via Google Cloud. For experimental structures use PDB; for prediction use ColabFold or ESMFold.
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