MolClaw: An Autonomous Agent with Hierarchical Skills for Drug Molecule Evaluation, Screening, and Optimization
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scppredmoladmet. Predict the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the input molecules.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scppredbindingaffinityboltz2. Predict binding affinity between target protein sequence and small molecule SMILES using Boltz-2.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpchai1predict. Predict protein structures with Chai-1 from sequence or FASTA input and return model scoring summaries.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpchromacomplex, mcpmolclaw-scpchromamonomer, mcpmolclaw-scpchromasymmetry. Chroma toolkit skill covering chromamonomer for single-chain generation, chromacomplex for multi-chain assembly generation, and chromasymmetry for symmetry-constrained protein design.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpretrievesmilesbycompoundname. Retrieve SMILES strings by compound name using PubChem with an NCI resolver fallback.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpreinventdenovosampling. Generate new molecules de novo.
Skill Claude CodeCodex
Note.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpcalculatedlepsscore. Calculate disease reversal scores for the provided molecules relative to a specific disease.
Skill Claude CodeCodex
High-level large-scale virtual screening workflow (10+ ligands) combining property filtering, QuickVina docking, EquiScore rescoring, and consensus ranking for target prioritization.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpcalculatemoldrugchemistry. Compute the drug-likeness metrics (QED score and Number of violations of Lipinski's Rule of Five) of the input candidate molecules (SMILES format).
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpconvertcomplexciftopdb, mcpmolclaw-scpconvertpdbtopdbqtdock, mcpmolclaw-scpconvertsmilestoformat. End-to-end docking-score ranking using EquiScore for candidate molecules against a target protein.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpequiscorepipeline, mcpmolclaw-scpequiscorepocket, mcpmolclaw-scpequiscorescreen. Unified EquiScore skill for pocket extraction, pocket scoring, and end-to-end docking-to-score pipeline execution.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scppredproteinstructureesmfold. Use ESMFold model to predict 3D structure of the input protein sequence.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpevobindtool. Design linear or cyclic peptide binders from receptor FASTA sequences using EvoBind2 with structured result outputs.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpextractandsavechains, mcpmolclaw-scpextractpdbchains. Extract protein sequence of each chain from the protein structure file (pdb format).
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpbase64toserverfile, mcpmolclaw-scpserverfiletobase64. Transfer files through the MCP client using a local path when supported, or Base64 directly.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpfixpdb. Repair and clean PDB or mmCIF structures with PDBFixer, returning a repaired PDB path and topology counts.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpfoldxtool. FoldX protein stability and mutation analysis tool. Supports 8 modes: structure repair (RepairPDB), stability calculation (Stability), mutation ΔΔG (BuildModel), complex interface energy (AnalyseComplex), alanine scanning (AlaScan), position scanning…
Skill Claude CodeCodex
Detect binding pockets with fpockettoolkit and return parsed pocket descriptors and run artifacts.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpfpockettoolkit. Use fpocket to detect binding pockets and output their detailed properties for the input protein. This offers a more concise approach to pocket identification.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpgocapipeline. Run GoCa coarse-grained protein MD pipeline and collect key simulation artifacts from a unified run directory.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scphdocktool. Run HDOCKlite docking for protein complexes and return run directories with ranked models.
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpinteractionvisualizer. PRIMARY tool for all single-structure interaction analysis. MCP-exposed protein–ligand / peptide / protein–protein interaction analysis and Schrödinger-style multi-dimensional visualization. Pure Python/NumPy engine covering 9 interaction…
Skill Claude CodeCodex
Use when calling these MolClaw MCP tools: mcpmolclaw-scpkarmadocktool. Run KarmaDock graph generation and virtual screening to produce ranked ligand poses and summary metrics.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: