'pdb' 검색 결과

Automate Abuselpdb operations through Rube MCP, a connection for agent tools. Discover available actions and their required inputs, verify the service connection, and execute tasks using the current tool definitions.

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• Finding available Abuselpdb actions
• Checking the connection before running tasks
• Automating repeated Abuselpdb operations

Automate Abuselpdb operations through Rube MCP, a connection for agent tools. Discover available actions and their required inputs, verify the service connection, and execute tasks using the current tool definitions.

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• Finding available Abuselpdb actions
• Checking the connection before running tasks
• Automating repeated Abuselpdb operations

Look up structure metadata in RCSB PDB, search for entries by keyword, and retrieve sequences in FASTA, a text format for biological sequences. Receive concise summaries or short sequence previews, with raw output available on request.

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• Check basic metadata for a known PDB entry
• Find structure entries using a keyword
• Retrieve an entry's sequences in FASTA format

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

Transfer known function and variable names from an older binary to a newer version. Compare disassembly and pseudocode with an LLM, produce structured mappings, and apply names and comments in IDA.

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• Migrate known function names after a software update
• Locate kernel functions when the new PDB is unavailable
• Find updated function addresses and structure offsets

Python 실행을 멈춰 변수와 코드 흐름을 살펴보며 버그 원인을 추적합니다. 예외 발생 당시의 상태와 실행 중인 프로세스도 확인할 수 있습니다.

• 실패한 Python 테스트의 변수를 확인합니다
• 예상하지 못한 상태 변화를 추적합니다
• 예외 발생 당시의 상태를 조사합니다

Investigate Python bugs by pausing execution, inspecting variables, and stepping through code. Choose pdb for local inspection or debugpy for remote connections, with guidance for failing tests, crash analysis, and already running processes.

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• Inspecting variables in a failing test
• Tracing changes to a collection inside a function
• Examining local variables at a crash site

Investigate suspicious IP addresses, domains, URLs, file hashes, and email artifacts using multiple threat intelligence sources. Assess confidence that each indicator is malicious, check links to known campaigns, and document evidence for blocking, monitoring, or allowing it.

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• Triaging indicators from phishing emails
• Investigating suspicious IP addresses and URLs in alerts
• Assessing bulk indicators before adding them to blocklists

Review GKE reliability settings for applications running in Kubernetes. Configure availability safeguards during maintenance, health checks, replica counts, graceful shutdown, and distribution across zones and nodes to help workloads handle disruptions.

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• Reviewing GKE high availability
• Maintaining Pod availability during upgrades
• Configuring application health checks

Prepare and run molecular dynamics simulations with OpenMM, then analyze molecular motion with MDAnalysis. Examine protein flexibility, structural changes, and protein–ligand contacts through calculations and plots of simulated trajectories.

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• Investigating protein stability after a mutation
• Measuring structural changes and flexibility
• Tracking protein–ligand contacts

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

Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.

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Query RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".

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Retrieve protein sequences, annotation, and structures from UniProtKB, the RCSB PDB, and AlphaFold DB. Use this skill to resolve a gene or protein name to a UniProt accession, pull sequences and FASTA files, find binding sites and domains, search the PDB by UniProt accession, sequence, ligand, or text, download mmCIF/PDB coordinates and biological assemblies, fetch AlphaFold models with their pLDDT confidence, and check whether a structure is actually usable before docking or simulating it. Also trigger on UniProt accessions, PDB ids, rest.uniprot.org, search.rcsb.org, files.rcsb.org, alphafold.ebi.ac.uk, id mapping, SEQRES, or missing residues.

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Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

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Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.

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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.

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AbuselPDB integration. Manage data, records, and automate workflows. Use when the user wants to interact with AbuselPDB data.

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Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design.

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Process DNA, RNA, and protein sequences with Biopython, convert biological files, and retrieve NCBI records. Supports batch workflows for sequence comparison, searches for similar sequences, protein structure analysis, and evolutionary trees.

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• Convert GenBank files to FASTA
• Calculate sequence length and GC content in batches
• Retrieve sequences and publication records from NCBI

Build an OpenCTI pipeline that adds external context to indicators of compromise, such as suspicious IP addresses. Connect intelligence services, relate indicators to known attackers and campaigns, and score confidence to help analysts prioritize investigations.

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• Deploying OpenCTI and configuring enrichment connectors
• Automatically adding context to suspicious IP addresses and domains
• Relating indicators to known attackers and campaigns

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.

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• Adding threat context to security alerts
• Processing indicators from phishing email submissions
• Standardizing bulk indicator lookups from threat feeds

Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.

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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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