InternScience/MolClaw - Page 2

molclaw-fpocket-toolkit-base

Detect binding pockets with fpocket_toolkit and return parsed pocket descriptors and run artifacts.

molclaw-karmadock-tool

Run KarmaDock graph generation and virtual screening to produce ranked ligand poses and summary metrics.

molclaw-mol-basic-metrics

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…

molclaw-mol-charge-metrics

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.

molclaw-mol-complexity-metrics

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.

molclaw-mol-hbond-metrics

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.

molclaw-mol-hydrophobicity-metrics

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.

molclaw-mol-opt-physchem

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.

molclaw-mol-structure-metrics

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…

molclaw-mol-topology-metrics

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…

molclaw-p2rank

Use P2Rank to locate binding pockets in the input protein. Unless specified by the user, prioritize using fpocket.

molclaw-pack-sidechains

Predicts full-atom sidechain conformations from backbone PDBs using AttnPacker for structure preparation workflows.

molclaw-prolif-docking

ProLIF docking-pose analysis skill for batch interaction fingerprints and interaction count summaries.

molclaw-prolif-md

ProLIF MD trajectory analysis skill for protein-ligand interaction fingerprints with frame slicing and residue controls.

molclaw-prolif-pdb

ProLIF static complex analysis skill for a single protein-ligand structure.

molclaw-prolif-protein-protein

ProLIF protein-protein trajectory analysis skill for interface interaction fingerprints and stability profiling.

molclaw-prolif-tool

Unified ProLIF analysis skill covering MD trajectories, docking poses, single complex structures, and protein-protein interfaces.

molclaw-proteinmpnn-tool

Design or score protein sequences from PDB structures using a ProteinMPNN workflow wrapper.

molclaw-pulchura-rebuild

Rebuilds incomplete protein PDB structures with PULCHRA for downstream docking and simulation preparation.

molclaw-sequence-valid-check

Check if the input protein sequence is valid.

molclaw-smiles-fg-editor

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…

molclaw-smiles-valid-check

Check if the input molecule SMILES string is valid.

pubmed-search

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".