Molclaw Boltz2 Affinity
Predict binding affinity between target protein sequence and small molecule SMILES using Boltz-2.
Molclaw Prolif Pdb
ProLIF static complex analysis skill for a single protein-ligand structure.
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 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 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 Chai1 Predict
Predict protein structures with Chai-1 from sequence or FASTA input and return model scoring summaries.
Molclaw Prolif Tool
Unified ProLIF analysis skill covering MD trajectories, docking poses, single complex structures, and protein-protein interfaces.
Mol 3d Viewer
将 SMILES 或化学名称转换为分子 3D 结构。支持生成 SDF 文件、3D 分子图片和可交互 HTML 网页（可旋转观察）。
Reaction Data Extraction
从 PDF 文献中提取化学反应数据，特别是反应条件优化信息。支持提取反应物、产物、催化剂、溶剂、温度、时间、产率等，并输出结构化 CSV 文件。使用 MinerU + NLP + 规则匹配进行精确提取。
Literature Parsing
将 PDF 文献转换为 Markdown 文件，并提取所有图表图片。使用 MinerU (opendatalab) 进行工业级高质量解析。
Pdf Dft Extractor
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Chem Data Extractor
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Iupac To Smiles
将 IUPAC 化学名称转换为 SMILES 字符串。完全使用 OPSIN API，支持聚合物智能解析。
Chemical File Converter
化学文件格式转换工具。支持 .xyz, .gjf (Gaussian), .mol, .sdf, .pdb, .mol2 等格式互转。使用 Open Babel 或 RDKit 进行转换。当用户提供化学文件并要求转换格式、生成不同格式的文件、或提到文件转换时触发。
Surface Tension Predictor
基于 SMILES 提供与 surfactant（表面活性剂）任务相关的表面张力参考预测，支持 baseline 启发式后端与 public_joblib 公开模型参考后端。
Molclaw Prolif Md
ProLIF MD trajectory analysis skill for protein-ligand interaction fingerprints with frame slicing and residue controls.
Molclaw Fpocket Toolkit Base
Detect binding pockets with fpocket_toolkit and return parsed pocket descriptors and run artifacts.
Molclaw Mol2mol Sampling
Generate new molecules sampling from the input molecule.
Molclaw Interaction Visualizer
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Molclaw Openawsem Tool
Runs OpenAWSEM simulations and extracts representative trajectory frames for downstream ensemble analysis.
Molclaw Prolif Docking
ProLIF docking-pose analysis skill for batch interaction fingerprints and interaction count summaries.
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 Foldx Tool
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Molclaw Fix Pdb
Repair and clean PDB files with PDBFixer, returning repaired file path and topology counts.
Molclaw Protein Structure Retrieve
Retrieve and download protein structure file (pdb format) using gene name, Uniprot ID or PDB ID.
Molclaw Prolif Protein Protein
ProLIF protein-protein trajectory analysis skill for interface interaction fingerprints and stability profiling.
Molclaw Protein Openmm
Run OpenMM protein MD and extract evenly spaced trajectory frames for downstream structural analysis.
Molclaw Goca Tool
Run GoCa coarse-grained protein MD pipeline and collect key simulation artifacts from a unified run directory.
Molclaw Evobind Tool
Design linear or cyclic peptide binders from receptor FASTA sequences using EvoBind2 with structured result outputs.
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.
Mineru Pdf Converter
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Molecular Properties Predictor
预测小分子多种物化性质（沸点、折射率、密度、黏度、表面张力等），当前已真实接入 bamboo_mixer 单分子物性模型后端。
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 well as the fraction of sp³-hybridized carbon atoms (Fsp³).
Geometry Optimizer
使用半经验方法 (xTB) 对分子三维结构进行几何优化，支持 SMILES 自动转 3D、XYZ 文件输入，输出优化后坐标、能量、收敛状态。
Raman Spectra Simulation
Compute and visualize Raman Spectra from input SMILES or XYZ file with MLatom.
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 shape indices (Kappa1–Kappa3) for each input molecule.
Molclaw Equiscore Docking
End-to-end docking-score ranking using EquiScore for candidate molecules against a target protein.
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.
Md Vib Spectra Simulation
Compute vibrational spectra from MD trajectory — power spectrum (velocity autocorrelation) or IR (dipole autocorrelation) via MLatom.
Molclaw Protein Ligand Mmpbsa
Execution-ready protein-ligand MM/GB(PB)SA workflow with explicit MCP handoffs and optional analysis.
Molclaw Protein Protein Mmpbsa
Execution-ready protein-protein MM/GB(PB)SA workflow with MCP-exposed tool names, strict file validation, and failure guards.
Molclaw Protein Sequence Retrieve
Search the target protein sequence information from the input gene name or uniprot id.
Gjf To Xyz
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Nmr Prediction
Predict liquid-phase ¹H and ¹³C NMR chemical shifts from a SMILES string using NMRNet (deep learning, SE(3)-Transformer). Outputs per-atom shift values (ppm) and Lorentzian-broadened spectrum PNG files.
Adme Prediction
ADME 性质预测工具。预测分子的吸收、分布、代谢、排泄性质，包括 Caco-2 通透性、PAMPA、HIA、Pgp 抑制、生物利用度、亲脂性等。使用 Morgan 指纹 + Random Forest/XGBoost。当用户提到 ADME 预测、药物性质、通透性、吸收、代谢等时触发。
Molclaw Equiscore Tool
Unified EquiScore skill for pocket extraction, pocket scoring, and end-to-end docking-to-score pipeline execution.
Molclaw Compound Retrieve
A Claude skill from InternScience/MolClaw.
Mol Image To Smiles
将分子结构图片转换为 SMILES 字符串。使用 DECIMER 和 MolNextR 模型进行图像识别。
Mol Paper Renderer
论文级分子渲染工具。使用 xyzrender 生成出版质量的 SVG、PNG、PDF 和 GIF 动画。支持过渡态、非共价相互作用、分子轨道、晶体结构等高级功能。
Molclaw Admet
Predict the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the input molecules.
Uv Vis Spectrum Simulation
UV-Vis spectrum from SMILES via UV-adVISor (https://spectra.collaborationspharma.com/). Input SMILES, auto-fetch, plot PNG.
Molclaw Peptide Sampling
Generate new peptide molecules sampling from the input peptide sequence.
Molclaw Esmfold
Use ESMFold model to predict 3D structure of the input protein sequence.
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.
Ms Spectra Simulation
Predict and visualize MS/MS spectra from a single SMILES using the fioRa online app. Use when the user wants a mass spectrum, MGF/MSP output, or a plotted stick spectrum from SMILES, with optional custom Name, precursor type, collision energy, and instrument settings.
Pka Predictor
预测小分子的 pKa，支持 custom 启发式后端和 Uni-pKa 单文件权重后端（Bohrium notebook 路线）。
Molclaw Pdbfixer
Repair a protein PDB file with PDBFixer: fix missing atoms/residues, add hydrogens, remove heterogens, etc.
Smiles To Iupac
将 SMILES 字符串转换为 IUPAC 化学名称。使用 PubChem、NCI/CADD、STOUT、RDKit-InChI 多种方法智能转换。
Molclaw Linker Sampling
Generate new molecules sampling from the input two warhead fragments.
Mol 2d Viewer
将 SMILES 或化学名称转换为分子 2D 结构图。支持普通分子和聚合物 2D 结构绘制。
Xrd Spectra Simulation
XRD spectrum from CIF structure file using pymatgen (Cu Kα).
Molclaw Extract Chains
Extract protein sequence of each chain from the protein structure file (pdb format).
Molclaw Pack Sidechains
Predicts full-atom sidechain conformations from backbone PDBs using AttnPacker for structure preparation workflows.
Molclaw File Transfer
Implement data transmission between the local computer and the MCP Server using Base64 encoding
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 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 Dleps
Calculate disease reversal scores for the provided molecules relative to a specific disease.
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 molecule.
Molclaw P2rank
Use P2Rank to locate binding pockets in the input protein. Unless specified by the user, prioritize using fpocket.
Ir Spectra Simulation
Compute and visualize IR Spectra from input SMILES or XYZ file with MLatom.
Molclaw Diffdock Auto
[CURRENTLY UNAVAILABLE] DiffDock protein-ligand docking. This tool is not deployed on the current MCP server. Use molclaw-quickvina-docking or molclaw-karmadock-tool as alternatives.
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.
Boron Nmr Predict
Predict 11B (boron-11) NMR chemical shift for boron-containing molecules using a local CPU inference pipeline. Use when the user asks to predict boron NMR or 11B chemical shift and provides a molecule such as a SMILES string. The skill can download model weights from Hugging Face on first use, run local CPU inference, and generate a labeled molecule image so each predicted shift can be matched to…
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 Denovo Sampling
Generate new molecules de novo.