Skills in diesem Repository
SkillsMP hat 67 Skills aus InternScience/MolClaw gesammelt. Öffne einen Skill, um Quelle und Details zu prüfen.
InternScience/MolClawEs werden 27 von 67 gesammelten Skills angezeigt.
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__retrieve_protein_sequence`. Search the target protein sequence information from the input gene name or uniprot id.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__retrieve_protein_structure_by_gene_name`, `mcp__molclaw-scp__retrieve_protein_structure_by_pdb_id`, `mcp__molclaw-scp__retrieve_protein_structure_by_uniprot_id`. Retrieve and download a protein…
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__proteinmpnn_tool`. Design or score protein sequences from PDB structures using a ProteinMPNN workflow wrapper.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__pulchura_rebuild`. Rebuilds incomplete protein PDB structures with PULCHRA for downstream docking and simulation preparation.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__molecule_docking_quickvina_fullprocess`. Perform molecular docking using QuickVina2-GPU between target protein structure and small molecules.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__residue_mapper`. Map residue indices among UniProt, PDB author numbering, and tool-internal numbering.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__libinvent_rgroup_sampling_by_scaffold`, `mcp__molclaw-scp__libinvent_rgroup_sampling_by_scaffold_name`. Generate new molecules sampling from the input scaffold.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__extract_bioemu_structures`, `mcp__molclaw-scp__run_bioemu`. Run BioEmu sequence sampling and extract ensemble structures for downstream conformation analysis.
Quellsprache: Englisch
Use the configured MolClaw MCP tools through Claude; direct Python SDK access is an optional fallback for standalone scripts.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__is_valid_protein_sequence`. Check if the input protein sequence is valid.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__is_valid_smiles`. Check if the input molecule SMILES string is valid.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__visualize_molecule`. Render a molecule from a SMILES string or a server-side molecular structure file with the MolClaw MCP tool `visualize_molecule`.
Quellsprache: Englisch
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__visualize_protein`. Render a server-side PDB protein structure as a PNG with the MolClaw MCP tool `visualize_protein`.
Quellsprache: Englisch
Formats extracted execution patterns into standard MolClaw skill documents. Accepts structured input from the Skill Crystallization Meta-Workflow (L2-12) and outputs a properly formatted L1 or L2 skill document conforming to MolClaw conventions. This skill…
Quellsprache: Englisch
Repair a protein PDB or mmCIF structure with PDBFixer and write a repaired PDB.
Quellsprache: Englisch
Execution-ready protein-ligand MM/GB(PB)SA workflow with explicit MCP handoffs and optional analysis.
Quellsprache: Englisch
Execution-ready protein-protein MM/GB(PB)SA workflow with MCP-exposed tool names, strict file validation, and failure guards.
Quellsprache: Englisch
[CURRENTLY UNAVAILABLE] DiffDock protein-ligand docking. This tool is not deployed on the current MCP server. Use molclaw-quickvina-docking or molclaw-karmadock-tool as alternatives.
Quellsprache: Englisch
High-level large-scale virtual screening workflow (10+ ligands) combining property filtering, QuickVina docking, EquiScore rescoring, and consensus ranking for target prioritization.
Quellsprache: Englisch
Detect binding pockets with fpocket_toolkit and return parsed pocket descriptors and run artifacts.
Quellsprache: Englisch
Integrating molecular property calculation tools with the reasoning capabilities of Large Language Models (LLMs) to optimize key physicochemical properties of drug molecules, such as LogP, QED, and solubility.
Quellsprache: Englisch
ProLIF docking-pose analysis skill for batch interaction fingerprints and interaction count summaries.
Quellsprache: Englisch
ProLIF MD trajectory analysis skill for protein-ligand interaction fingerprints with frame slicing and residue controls.
Quellsprache: Englisch
ProLIF static complex analysis skill for a single protein-ligand structure.
Quellsprache: Englisch
ProLIF protein-protein trajectory analysis skill for interface interaction fingerprints and stability profiling.
Quellsprache: Englisch
Edit molecular structures in SMILES notation by adding, deleting, or replacing functional groups. Use this skill whenever the user asks to modify a molecule's SMILES by manipulating functional groups (e.g., "delete hydroxyl", "add nitrile", "replace amine…
Quellsprache: Englisch
Search PubMed for scientific literature. Use when the user asks to find papers, search literature, look up research, find publications, or asks about recent studies. Triggers on "pubmed", "papers", "literature", "publications", "research on", "studies about".
Quellsprache: Englisch