InternScience/Agents-A1

molclaw-admet

Predict the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the input molecules.

molclaw-boltz2-affinity

Predict binding affinity between target protein sequence and small molecule SMILES using Boltz-2.

molclaw-chai1-predict

Predict protein structures with Chai-1 from sequence or FASTA input and return model scoring summaries.

molclaw-chroma-toolkit

Chroma toolkit skill covering chroma_monomer for single-chain generation, chroma_complex for multi-chain assembly generation, and chroma_symmetry for symmetry-constrained protein design.

molclaw-compound-retrieve

Retrieve SMILES strings from PubChem database using compound names.

molclaw-denovo-sampling

Generate entirely new drug-like molecules from scratch without any starting molecule, using REINVENT4's de novo prior.

molclaw-diffdock-auto

Run automated DiffDock protein-ligand docking and return confidence-based result summaries.

molclaw-dleps

Calculate disease reversal scores for the provided molecules relative to a specific disease.

molclaw-docking-screening

High-level large-scale virtual screening workflow (10+ ligands) combining property filtering, QuickVina docking, EquiScore rescoring, and consensus ranking for target prioritization.

molclaw-drug-likeness

Compute the drug-likeness metrics (QED score and Number of violations of Lipinski's Rule of Five) of the input candidate molecules (SMILES format).

molclaw-equiscore-docking

End-to-end docking-score ranking using EquiScore for candidate molecules against a target protein.

molclaw-equiscore-tool

Unified EquiScore skill for pocket extraction, pocket scoring, and end-to-end docking-to-score pipeline execution.

molclaw-esmfold

Use ESMFold model to predict 3D structure of the input protein sequence.

molclaw-evobind-tool

Design linear or cyclic peptide binders from receptor FASTA sequences using EvoBind2 with structured result outputs.

molclaw-extract-chains

Extract protein sequence of each chain from the protein structure file (pdb format).

molclaw-file-transfer

Implement data transmission between the local computer and the MCP Server using Base64 encoding

molclaw-fix-pdb

Repair and clean PDB files with PDBFixer, returning repaired file path and topology counts.

molclaw-fpocket

Use fpocket to detect binding pockets and output their detailed properties for the input protein. This offers a more concise approach to pocket identification.

molclaw-fpocket-toolkit-base

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

molclaw-goca-tool

Run GoCa coarse-grained protein MD pipeline and collect key simulation artifacts from a unified run directory.

molclaw-hdock-tool

Run HDOCKlite docking for protein complexes and return run directories with ranked models.

molclaw-karmadock-tool

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

molclaw-linker-sampling

Generate linker molecules connecting two warhead fragments, for applications such as PROTAC design, bivalent ligands, and fragment merging.

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-opt-target

Optimize drug molecular structures to enhance binding activity against specific protein targets, using binding assessment tools, interaction analysis, and LLM-guided molecular design.

molclaw-mol-similarity

Calculate both Tanimoto similarities and the count of shared structural fragments between a target molecule and a list of candidate molecules via Morgan fingerprints.

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-mol2mol-sampling

Generate new molecules by transforming an input molecule using different priors for scaffold-aware, similarity-controlled molecular optimization.

molclaw-openawsem-tool

Runs OpenAWSEM simulations and extracts representative trajectory frames for downstream ensemble analysis.

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-pdbfixer

Repair a protein PDB file with PDBFixer: fix missing atoms/residues, add hydrogens, remove heterogens, etc.

molclaw-peptide-sampling

Generate peptide molecules using PepInvent, supporting template-based generation, custom peptide sequence modification, and info queries for available templates and amino acids.

molclaw-prolif-docking

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