InternScience/Agents-A1

molclaw-admet

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

Quellsprache: Englisch

molclaw-boltz2-affinity

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

Quellsprache: Englisch

molclaw-chai1-predict

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

molclaw-compound-retrieve

Retrieve SMILES strings from PubChem database using compound names.

Quellsprache: Englisch

molclaw-denovo-sampling

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

Quellsprache: Englisch

molclaw-diffdock-auto

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

Quellsprache: Englisch

molclaw-dleps

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

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).

Quellsprache: Englisch

molclaw-equiscore-docking

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

Quellsprache: Englisch

molclaw-equiscore-tool

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

Quellsprache: Englisch

molclaw-esmfold

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

Quellsprache: Englisch

molclaw-evobind-tool

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

Quellsprache: Englisch

molclaw-extract-chains

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

Quellsprache: Englisch

molclaw-file-transfer

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

Quellsprache: Englisch

molclaw-fix-pdb

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

molclaw-fpocket-toolkit-base

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

Quellsprache: Englisch

molclaw-goca-tool

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

Quellsprache: Englisch

molclaw-hdock-tool

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

Quellsprache: Englisch

molclaw-karmadock-tool

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

Quellsprache: Englisch

molclaw-linker-sampling

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

Quellsprache: Englisch

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…

Quellsprache: Englisch

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.

Quellsprache: Englisch

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.

Quellsprache: Englisch

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.

Quellsprache: Englisch

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.

Quellsprache: Englisch

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.

Quellsprache: Englisch

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.

Quellsprache: Englisch

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.

Quellsprache: Englisch

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…

Quellsprache: Englisch

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…

Quellsprache: Englisch

molclaw-mol2mol-sampling

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

Quellsprache: Englisch

molclaw-openawsem-tool

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

Quellsprache: Englisch

molclaw-p2rank

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

Quellsprache: Englisch

molclaw-pack-sidechains

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

Quellsprache: Englisch

molclaw-pdbfixer

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

Quellsprache: Englisch

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.

Quellsprache: Englisch

molclaw-prolif-docking

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

Quellsprache: Englisch