internscience
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- ▌ Manim · internscience bundleComprehensive guide for Manim Community - Python framework for creating mathematical animations and educational videos with programmatic control
- ▌ Github · internscience bundleInteract with GitHub using the `gh` CLI. Use `gh issue`, `gh pr`, `gh run`, and `gh api` for issues, PRs, CI runs, and advanced queries.
- ▌ Scientific Slides · internscience bundleBuild slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
- ▌ Arxiv Watcher · internscience bundleSearch and summarize papers from ArXiv. Use when the user asks for the latest research, specific topics on ArXiv, or a daily summary of AI papers.
- ▌ Markdown Converter · internscience bundleConvert documents and files to Markdown using markitdown. Use when converting PDF, Word (.docx), PowerPoint (.pptx), Excel (.xlsx, .xls), HTML, CSV, JSON, XML, images (with EXIF/OCR), audio (with transcription), ZIP archives, YouTube URLs, or EPubs to Markdown format for LLM processing or text analysis.
- ▌ Scientific Visualization · internscience bundleMeta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
- ▌ Local Skill Hub 2 · internscienceManage dormant local skill templates and attach them to equipment agents.
- ▌ Scientific Brainstorming · internscience bundleCreative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.
- ▌ Scientific Critical Thinking · internscience bundleEvaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.
- ▌ Graphanything · internscience bundleTurn anything into a navigable knowledge graph. 10 schema presets, 8 extractors (markdown / json-yaml / openapi / fstree / chatlog / LLM-entity / VLM-stub / noop), human-in-the-loop review.
- ▌ Gjf To Xyz · internscience bundleConvert Gaussian gjf input files to XYZ format. 将Gaussian gjf输入文件转换为XYZ格式。 Use when agent needs to convert molecular structure files from Gaussian input format (.gjf) to XYZ format for visualization or use with other computational chemistry software. 当智能体需要将Gaussian输入格式(.gjf)的分子结构文件转换为XYZ格式用于可视化或其他计算化学软件时使用。
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- ▌ Mol 3d Viewer · internscience bundle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）。
- ▌ Pka Predictor · internscience bundle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）。
- ▌ Nmr Prediction · internscience bundlePredict 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 · internscience bundleADME 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。
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- ▌ Smiles To Iupac · internscience bundle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。
- ▌ Boron Nmr Predict · internscience bundlePredict 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 a specific boron atom.
- ▌ PDF Dft Extractor · internscience bundleExtract DFT calculation coordinates from PDF files and generate Gaussian gjf files. 从PDF文件中提取DFT计算坐标并生成Gaussian gjf输入文件。 Supports batch processing with separate output folders for each PDF. 支持批量处理，每个PDF单独生成输出文件夹。
- ▌ Geometry Optimizer · internscience bundle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。
- ▌ Literature Parsing · internscience bundle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。
- ▌ Mol Paper Renderer · internscience bundle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。
- ▌ Chem Data Extractor · internscience bundleExtract structured chemical compound characterization data from chemistry supplementary material documents (PDF/Markdown). 从化学论文补充材料(PDF/Markdown)中提取结构化化合物表征数据。 Use when Kimi needs to extract compound properties including NMR spectra, HRMS, HPLC data, melting points, optical rotation, and yield information from chemistry research papers or supplementary materials. 支持提取NMR谱图、HRMS、HPLC数据、熔点、旋光度、产率等信息。 Supports both single compound extraction and batch extraction of all compounds. 支持单个化合物提取和批量提取所有化合物。
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- ▌ Mineru PDF Converter · internscience bundleConvert PDF files to Markdown using MinerU API. 使用MinerU API将PDF文件转换为Markdown格式。 Use when Kimi needs to extract structured text, images, tables, and formulas from PDF documents while preserving document layout and formatting. 适用于需要提取结构化文本、图片、表格和公式并保留文档布局的场景。 Supports batch conversion and outputs full.md with images/, JSON metadata, and other extracted assets. 支持批量转换，输出full.md、images/目录、JSON元数据等。 Now supports large PDFs (600+ pages) by automatic splitting and merging. 现已支持大文件(600+页)自动拆分和合并处理。
- ▌ Ir Spectra Simulation · internscience bundleCompute and visualize IR Spectra from input SMILES or XYZ file with MLatom.
- ▌ Ms Spectra Simulation · internscience bundlePredict 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.
- ▌ Xrd Spectra Simulation · internscience bundleXRD spectrum from CIF structure file using pymatgen (Cu Kα).
- ▌ Chemical File Converter · internscience bundle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。
- ▌ Raman Spectra Simulation · internscience bundleCompute and visualize Raman Spectra from input SMILES or XYZ file with MLatom.
- ▌ Reaction Data Extraction · internscience bundle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。
- ▌ Md Vib Spectra Simulation · internscience bundleCompute vibrational spectra from MD trajectory — power spectrum (velocity autocorrelation) or IR (dipole autocorrelation) via MLatom.
- ▌ Surface Tension Predictor · internscience bundle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。
- ▌ Uv Vis Spectrum Simulation · internscience bundleUV-Vis spectrum from SMILES via UV-adVISor (https://spectra.collaborationspharma.com/). Input SMILES, auto-fetch, plot PNG.
- ▌ Molecular Properties Predictor · internscience bundle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 Opt Target · internscience bundleOptimize drug molecular structures to enhance binding activity against specific protein targets, using binding assessment tools, interaction analysis, and LLM-guided molecular design.
- ▌ Molclaw Residue Mapper · internscienceMap residue numbering between UniProt canonical, PDB author, and tool-internal sequential numbering schemes. Essential for correctly interpreting ProLIF/PLIP results from predicted structures (ESMFold, Boltz-2, Chai-1) and RCSB PDB files with non-trivial numbering offsets. Prevents silent misinterpretation of residue-specific analysis outputs.
- ▌ Molclaw Rgroup Optimization · internscienceGoal-directed R-group optimization using reinforcement learning. Generates scaffold-decorated molecules optimized toward QED, property constraints, and optional similarity targets, with R-group-level controls.
- ▌ Molclaw Similarity Optimization · internscienceGoal-directed molecular optimization using reinforcement learning (staged_learning). Generates molecules similar to a target while optimizing multiple physicochemical properties simultaneously via weighted scoring components.
- ▌ Molclaw Equiscore Docking · internscienceEnd-to-end docking-score ranking using EquiScore for candidate molecules against a target protein.
- ▌ Molclaw Mol Basic Metrics · internscienceCompute 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 Mol Hbond Metrics · internscienceCompute 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 Quickvina Docking · internsciencePerform molecular docking using QuickVina2-GPU between target protein structure and small molecules.
- ▌ Molclaw Visualize Protein · internscienceRender a server-side PDB protein structure as a PNG with the MolClaw MCP tool `visualize_protein`.
- ▌ Molclaw Mol Charge Metrics · internscienceCompute 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.
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- ▌ Molclaw Visualize Molecule · internscienceRender a molecule from a SMILES string or a server-side molecular structure file with the MolClaw MCP tool `visualize_molecule`.
- ▌ Molclaw Fpocket Toolkit Base · internscienceDetect binding pockets with fpocket_toolkit and return parsed pocket descriptors and run artifacts.
- ▌ Molclaw Mol Topology Metrics · internscienceCompute 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.
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- ▌ Molclaw Mol Structure Metrics · internscienceCompute 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).
- ▌ Molclaw Protein Ligand Mmpbsa · internscience bundleExecution-ready protein-ligand MM/GB(PB)SA workflow with explicit MCP handoffs and optional analysis.
- ▌ Molclaw Skill Template Writer · internscienceFormats extracted execution patterns into standard MolClaw skill documents. Accepts structured input from the Skill Crystallization Meta-Workflow (L2-12) and outputs a properly formatted L1 or L2 skill document conforming to MolClaw conventions. This skill ensures that auto-generated skills are structurally identical to expert-curated skills, enabling seamless integration into the skill matching and loading pipeline.
- ▌ Molclaw Interaction Visualizer · internscience bundle**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, interface network, and decision-ready CSV/JSON export. Always use this tool first; fall back to ProLIF MCP only for batch docking fingerprint comparison or MD trajectory analysis.
- ▌ Molclaw Mol Complexity Metrics · internscienceCompute 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 Prolif Protein Protein · internscienceProLIF protein-protein trajectory analysis skill for interface interaction fingerprints and stability profiling.
- ▌ Molclaw Protein Protein Mmpbsa · internscience bundleExecution-ready protein-protein MM/GB(PB)SA workflow with MCP-exposed tool names, strict file validation, and failure guards.
- ▌ Molclaw Protein Sequence Retrieve · internscienceSearch the target protein sequence information from the input gene name or uniprot id.
- ▌ Molclaw Mol Hydrophobicity Metrics · internscienceComputes 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 Protein Structure Retrieve · internscienceRetrieve and download a protein structure file (.pdb or .cif) using a gene name, UniProt ID, or PDB ID.
- ▌ Molclaw Admet · internsciencePredict the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the input molecules.
- ▌ Molclaw Dleps · internscienceCalculate disease reversal scores for the provided molecules relative to a specific disease.
- ▌ Molclaw P2rank · internscienceUse P2Rank to locate binding pockets in the input protein. Unless specified by the user, prioritize using fpocket.
- ▌ Molclaw Esmfold · internscienceUse ESMFold model to predict 3D structure of the input protein sequence.
- ▌ Molclaw Fix Pdb · internscienceRepair and clean PDB or mmCIF structures with PDBFixer, returning a repaired PDB path and topology counts.
- ▌ Molclaw Fpocket · internscienceUse fpocket to detect binding pockets and output their detailed properties for the input protein. This offers a more concise approach to pocket identification.
- ▌ Molclaw Pdbfixer · internscienceRepair a protein PDB or mmCIF structure with PDBFixer and write a repaired PDB.
- ▌ Molclaw Goca Tool · internscienceRun GoCa coarse-grained protein MD pipeline and collect key simulation artifacts from a unified run directory.
- ▌ Molclaw Prolif Md · internscienceProLIF MD trajectory analysis skill for protein-ligand interaction fingerprints with frame slicing and residue controls.
- ▌ Molclaw Foldx Tool · internscienceFoldX protein stability and mutation analysis tool. Supports 8 modes: structure repair (RepairPDB), stability calculation (Stability), mutation ΔΔG (BuildModel), complex interface energy (AnalyseComplex), alanine scanning (AlaScan), position scanning (PositionScan), PSSM generation (Pssm), and per-residue energy decomposition (SequenceDetail). Covers fast empirical force-field evaluation between geometric analysis (interaction-visualizer) and full MD simulation (MMPBSA).
- ▌ Molclaw Hdock Tool · internscienceRun HDOCKlite docking for protein complexes and return run directories with ranked models.
- ▌ Molclaw Prolif Pdb · internscienceProLIF static complex analysis skill for a single protein-ligand structure.
- ▌ Molclaw Run Bioemu · internscienceRun BioEmu sequence sampling and extract ensemble structures for downstream conformation analysis.
- ▌ Molclaw Scp Server · internscienceAll tools utilized within MolClaw skills connect via the MCP protocol. This skill is the unified guide for connecting to the deployed MCP server before invoking tools.
- ▌ Molclaw Prolif Tool · internscienceUnified ProLIF analysis skill covering MD trajectories, docking poses, single complex structures, and protein-protein interfaces.
- ▌ Molclaw Evobind Tool · internscienceDesign linear or cyclic peptide binders from receptor FASTA sequences using EvoBind2 with structured result outputs.
- ▌ Molclaw Chai1 Predict · internsciencePredict protein structures with Chai-1 from sequence or FASTA input and return model scoring summaries.
- ▌ Molclaw Diffdock Auto · internscience[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 Drug Likeness · internscienceCompute the drug-likeness metrics (QED score and Number of violations of Lipinski's Rule of Five) of the input candidate molecules (SMILES format).
- ▌ Molclaw File Transfer · internscienceImplement data transmission between the local computer and the MCP Server using Base64 encoding
- ▌ Molclaw Chroma Toolkit · internscienceChroma 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 Equiscore Tool · internscienceUnified EquiScore skill for pocket extraction, pocket scoring, and end-to-end docking-to-score pipeline execution.
- ▌ Molclaw Extract Chains · internscienceExtract protein sequence of each chain from the protein structure file (pdb format).
- ▌ Molclaw Karmadock Tool · internscienceRun KarmaDock graph generation and virtual screening to produce ranked ligand poses and summary metrics.
- ▌ Molclaw Mol Similarity · internscienceCalculate both Tanimoto similarities and the count of shared structural fragments between a target molecule and a list of candidate molecules via Morgan fingerprints.
- ▌ Molclaw Openawsem Tool · internscienceRuns OpenAWSEM simulations and extracts representative trajectory frames for downstream ensemble analysis.
- ▌ Molclaw Prolif Docking · internscienceProLIF docking-pose analysis skill for batch interaction fingerprints and interaction count summaries.
- ▌ Molclaw Protein Openmm · internscienceRun OpenMM protein MD and extract evenly spaced trajectory frames for downstream structural analysis.
- ▌ Pubmed Search · internscienceSearch 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".
- ▌ Molclaw Boltz2 Affinity · internsciencePredict binding affinity between target protein sequence and small molecule SMILES using Boltz-2.
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- ▌ Molclaw Linker Sampling · internscienceGenerate new molecules sampling from the input two warhead fragments.
- ▌ Molclaw Pack Sidechains · internsciencePredicts full-atom sidechain conformations from backbone PDBs using AttnPacker for structure preparation workflows.
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- ▌ Molclaw Mol Opt Physchem · internscienceIntegrating 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.
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- ▌ Molclaw Peptide Sampling · internscienceGenerate new peptide molecules sampling from the input peptide sequence.
- ▌ Molclaw Proteinmpnn Tool · internscienceDesign or score protein sequences from PDB structures using a ProteinMPNN workflow wrapper.
- ▌ Molclaw Pulchura Rebuild · internscienceRebuilds incomplete protein PDB structures with PULCHRA for downstream docking and simulation preparation.