115 skills · sorted by relevance
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.
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.
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.
Design protein sequences while accounting for bound small molecules, nucleic acids, or metals. Use LigandMPNN to redesign binding pockets or metal-coordinating sites, and export sequence files alongside PDB structures with the designed sequences applied.
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.
Design amino acid sequences from a protein backbone stored in a PDB file using ProteinMPNN. Generate multiple candidates, redesign selected chains while preserving specified residues, and vary sampling settings to prepare sequences for downstream structure prediction.
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.
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.
Investigate Python bugs by pausing execution, inspecting variables, and stepping through code. Choose between local debugging with pdb or breakpoint(), exception inspection, and connecting debugpy to remote or already running processes.
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.
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.
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.
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.
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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Predict how a small molecule may sit within a protein using structural inputs. Generate ranked 3D poses without defining a search region, then use those poses as starting points for further evaluation.
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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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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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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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.
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.