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Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__pred_mol_admet`. Predict the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the input molecules.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__pred_binding_affinity_boltz2`. Predict binding affinity between target protein sequence and small molecule SMILES using Boltz-2.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__chai1_predict`. Predict protein structures with Chai-1 from sequence or FASTA input and return model scoring summaries.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__chroma_complex`, `mcp__molclaw-scp__chroma_monomer`, `mcp__molclaw-scp__chroma_symmetry`. Chroma toolkit skill covering chroma_monomer for single-chain generation, chroma_complex for multi-chain…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__retrieve_smiles_by_compoundname`. Retrieve SMILES strings by compound name using PubChem with an NCI resolver fallback.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__reinvent_denovo_sampling`. Generate new molecules de novo.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_dleps_score`. Calculate disease reversal scores for the provided molecules relative to a specific disease.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_mol_drug_chemistry`. Compute the drug-likeness metrics (QED score and Number of violations of Lipinski's Rule of Five) of the input candidate molecules (SMILES format).
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__convert_complex_cif_to_pdb`, `mcp__molclaw-scp__convert_pdb_to_pdbqt_dock`, `mcp__molclaw-scp__convert_smiles_to_format`. End-to-end docking-score ranking using EquiScore for candidate molecules…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__equiscore_pipeline`, `mcp__molclaw-scp__equiscore_pocket`, `mcp__molclaw-scp__equiscore_screen`. Unified EquiScore skill for pocket extraction, pocket scoring, and end-to-end docking-to-score…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__pred_protein_structure_esmfold`. Use ESMFold model to predict 3D structure of the input protein sequence.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__evobind_tool`. Design linear or cyclic peptide binders from receptor FASTA sequences using EvoBind2 with structured result outputs.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__extract_and_save_chains`, `mcp__molclaw-scp__extract_pdb_chains`. Extract protein sequence of each chain from the protein structure file (pdb format).
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__base64_to_server_file`, `mcp__molclaw-scp__server_file_to_base64`. Transfer files through the MCP client using a local path when supported, or Base64 directly.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__fix_pdb`. Repair and clean PDB or mmCIF structures with PDBFixer, returning a repaired PDB path and topology counts.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__foldx_tool`. FoldX protein stability and mutation analysis tool. Supports 8 modes: structure repair (RepairPDB), stability calculation (Stability), mutation ΔΔG (BuildModel), complex interface…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__fpocket_toolkit`. Use fpocket to detect binding pockets and output their detailed properties for the input protein. This offers a more concise approach to pocket identification.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__goca_pipeline`. Run GoCa coarse-grained protein MD pipeline and collect key simulation artifacts from a unified run directory.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__hdock_tool`. Run HDOCKlite docking for protein complexes and return run directories with ranked models.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__interaction_visualizer`. **PRIMARY tool for all single-structure interaction analysis.** MCP-exposed protein–ligand / peptide / protein–protein interaction analysis and Schrödinger-style…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__karmadock_tool`. Run KarmaDock graph generation and virtual screening to produce ranked ligand poses and summary metrics.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__linkinvent_linker_sampling_by_warhead_pair_name`, `mcp__molclaw-scp__linkinvent_linker_sampling_by_warheads`. Generate new molecules sampling from the input two warhead fragments.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__analyze_mmpbsa`, `mcp__molclaw-scp__gmx_mmpbsa_propro`, `mcp__molclaw-scp__prepare_complex`, `mcp__molclaw-scp__prepare_protein_md`, `mcp__molclaw-scp__run_mmpbsa`. Prepare, run, and analyze…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_mol_basic_info`. Compute a set of basic molecular properties for a given list of SMILES strings, returning the molecular formula, exact and average molecular weights, counts of heavy and…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_mol_charge`. Compute Gasteiger partial charges and formal charge for a list of SMILES strings, returning the minimum, maximum, average, and range of the Gasteiger charges alongside the…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_mol_complexity`. Compute custom molecular complexity-related descriptors for a given list of SMILES strings, returning the molecular complexity score, aromatic proportion, and asphericity…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_mol_hbond`. Compute hydrogen bonding-related properties for a list of SMILES strings, specifically determining the number of hydrogen bond donors and acceptors for each input molecule.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_mol_hydrophobicity`. Computes hydrophobicity-related molecular descriptors for a given list of SMILES strings, returning the octanol-water partition coefficient (logP) and molar…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_common_fragments`, `mcp__molclaw-scp__calculate_morgan_fingerprint_similarity`. Calculate both Tanimoto similarities and the count of shared structural fragments between a target molecule…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_mol_structure_complexity`. Compute a set of molecular structure complexity descriptors for a list of SMILES strings, returning detailed metrics for each molecule including the number of…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_mol_topology`. Compute a comprehensive set of topological descriptors for a list of SMILES strings, returning the Topological Polar Surface Area (TPSA), a series of valence and non-valence…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__reinvent_mol2mol_sampling`. Generate new molecules sampling from the input molecule.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__openawsem_sim`, `mcp__molclaw-scp__openawsem_traj_extract`. Runs OpenAWSEM simulations and extracts representative trajectory frames for downstream ensemble analysis.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__pred_pocket_prank`. Use P2Rank to locate binding pockets in the input protein. Unless specified by the user, prioritize using fpocket.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__pack_sidechains`. Predicts full-atom sidechain conformations from backbone PDBs using AttnPacker for structure preparation workflows.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__get_pepinvent_info`, `mcp__molclaw-scp__pepinvent_peptide_sampling_by_peptide`, `mcp__molclaw-scp__pepinvent_peptide_sampling_by_template`. Generate new peptide molecules sampling from the input…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__prolif_docking`, `mcp__molclaw-scp__prolif_md`, `mcp__molclaw-scp__prolif_pdb`, `mcp__molclaw-scp__prolif_protein_protein`. Unified ProLIF analysis skill covering MD trajectories, docking poses,…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__analyze_protein_ligand_interactions`. Analyze protein-small-molecule contacts, interaction types, pocket composition, and steric clashes from a complex PDB.
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__calculate_pdb_basic_info`, `mcp__molclaw-scp__calculate_pdb_composition_info`, `mcp__molclaw-scp__calculate_pdb_quality_metrics`, `mcp__molclaw-scp__calculate_pdb_structural_geometry`,…
Idioma do texto original: inglês
Use when calling these MolClaw MCP tools: `mcp__molclaw-scp__openmm_extract_frames`, `mcp__molclaw-scp__protein_openmm_md`. Run OpenMM protein MD and extract evenly spaced trajectory frames for downstream structural analysis.
Idioma do texto original: inglês
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