Skill Claude CodeCodex
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 types with 2D diagram, 3D PyMOL rendering, residue bar, interface heatmap…
Skill Claude CodeCodex
Run KarmaDock graph generation and virtual screening to produce ranked ligand poses and summary metrics.
Skill Claude CodeCodex
Generate new molecules sampling from the input two warhead fragments.
Skill Claude CodeCodex
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 total atoms, number of bonds, valence electrons, and formal charge for each input molecule.
Skill Claude CodeCodex
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 formal charge for each molecule.
Skill Claude CodeCodex
Compute custom molecular complexity-related descriptors for a given list of SMILES strings, returning the molecular complexity score, aromatic proportion, and asphericity value for each input molecule.
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
Computes hydrophobicity-related molecular descriptors for a given list of SMILES strings, returning the octanol-water partition coefficient (logP) and molar refractivity for each input molecule.
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
Calculate both Tanimoto similarities and the count of shared structural fragments between a target molecule and a list of candidate molecules via Morgan fingerprints.
Skill Claude CodeCodex
Compute a set of molecular structure complexity descriptors for a list of SMILES strings, returning detailed metrics for each molecule including the number of rotatable bonds, total/aromatic/aliphatic/saturated rings, heteroatoms, and bridgehead atoms, as well as the fraction of sp³-hybridized carbon atoms (Fsp³).
Skill Claude CodeCodex
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 molecular connectivity indices (Chi0–Chi4), the Hall–Kier alpha value, and Kappa shape indices (Kappa1–Kappa3) for each input molecule.
Skill Claude CodeCodex
Generate new molecules sampling from the input molecule.
Skill Claude CodeCodex
Runs OpenAWSEM simulations and extracts representative trajectory frames for downstream ensemble analysis.
Skill Claude CodeCodex
Use P2Rank to locate binding pockets in the input protein. Unless specified by the user, prioritize using fpocket.
Skill Claude CodeCodex
Predicts full-atom sidechain conformations from backbone PDBs using AttnPacker for structure preparation workflows.
Skill Claude CodeCodex
Repair a protein PDB or mmCIF structure with PDBFixer and write a repaired PDB.
Skill Claude CodeCodex
Generate new peptide molecules sampling from the input peptide sequence.
Skill Claude CodeCodex
ProLIF docking-pose analysis skill for batch interaction fingerprints and interaction count summaries.
Skill Claude CodeCodex
ProLIF MD trajectory analysis skill for protein-ligand interaction fingerprints with frame slicing and residue controls.
Skill Claude CodeCodex
ProLIF static complex analysis skill for a single protein-ligand structure.
Skill Claude CodeCodex
ProLIF protein-protein trajectory analysis skill for interface interaction fingerprints and stability profiling.
Skill Claude CodeCodex
Unified ProLIF analysis skill covering MD trajectories, docking poses, single complex structures, and protein-protein interfaces.
Skill Claude CodeCodex
Execution-ready protein-ligand MM/GB(PB)SA workflow with explicit MCP handoffs and optional analysis.