Science & Research
723 results
- Academic SearchHyunjunJeonSearch academic paper repositories (arXiv, Semantic Scholar) for scholarly articles in physics, mathematics, computer science, quantitative biology, AI/ML, and related fields
- Math Modeling Skillanticipate218数学建模竞赛全流程助手：审题选题、模型选型与求解、结果检验（误差/灵敏度/稳健性）、论文写作与提交自检， 覆盖国赛 CUMCM、研赛华为杯、美赛 MCM/ICM。当用户准备建模竞赛、写建模论文、问赛题思路、写摘要、 做灵敏度分析、选模型、检查论文格式或提交前自检时使用——即使没说"数学建模"三字也应使用。
- Plot StylingneuromechanistThis skill should be used when the user asks to "plot data", "make a plot for a paper", "make a publication plot", "create a journal-quality plot", "matplotlib for a figure", "use seaborn", "use plotnine", "use ggplot in Python", "improve plot quality", "style my plot", "clean up my figure", "my matplotlib plot looks ugly", "apply journal style to existing script", "fix matplotlib defaults"…
- Mathmodel Studioyan315598-design数学建模竞赛助手：审题、附件检查、模型选型与实验、求解验证、科研绘图、论文整理和提交检查。支持研究生赛、国赛、华数杯、MCM/ICM、电工杯和亚太杯；也可只处理已有题目、结果或论文的局部任务。
- Game Godot SpecialistAlterLab Creative Technologies LaboratoryInvoke when the user works with Godot Engine or asks about GDScript, scene composition, signals, resources, shaders, GDExtension, physics, or Godot UI. Triggers on: "Godot", "GDScript", "scene tree", "signals", ".tscn", ".tres", "GDExtension", "project.godot".
- Paper Searchcabbage2000-lab文献检索与综述辅助命令。当用户已有研究问题（RQ）或明确方向，要查文献、做文献综述、找研究缺口（Research Gap）、了解"某方向别人做到哪一步"时使用——即使用户只说"帮我查查这方面的研究""这个领域有哪些论文""有没有人研究过 X""这方面国内外做到什么程度了""帮我搜搜文献""顺着这篇的参考文献往下找""谁引用了这篇""某某老师 / 这位作者发过哪些论文" "这几篇是不是同一个人写的""这些能不能免费下载 / 有没有全文""哪几篇是开放获取（OA）的""有没有 PMC 全文"也应使用。中英双轨：英文接开放 API（Crossref / OpenAlex / Semantic Scholar / arXiv）自动检索，中文走"自动 + 引导"（DOI 命中自动检索，其余生成知网 / 万方检索方案引导用户检索，站内官方导出的 BibTex / EndNote 文件可解析入表）。
- AdaptyvK-DenseHow to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization.
- Admet PredictionK-DenseTurn a set of structures into absorption, distribution, metabolism, excretion, and toxicity estimates with ADMET-AI, and read them as a developability verdict rather than a table of numbers. Use this skill to run batch prediction over a library, interpret each endpoint against its DrugBank-approved percentile, and flag the liabilities that stop a series — hERG blockade, CYP inhibition, poor…
- Binding Site AnalysisK-DenseDecide whether a protein has a pocket worth targeting, and where it is, before committing to a docking or design campaign. Use this skill to run fpocket cavity detection, rank cavities by druggability and volume, compare apo and holo conformations to spot induced fit, identify allosteric and cryptic cavities that only open in simulation, and convert a chosen cavity into the search box…
- BoltzK-DenseCofold protein-ligand, protein-protein, and nucleic-acid complexes with Boltz-2, and predict binding affinity with its trained affinity head. Use this skill to build Boltz input YAML, run structure prediction with MSAs, pocket constraints, templates, and modified residues, screen compound libraries by cofolding, and interpret confidence scores (pLDDT, pTM, ipTM, PDE) and affinity output (binder…
- ChemblK-DenseQuery the ChEMBL database web services for measured bioactivity data, compound records and calculated properties, targets, assays, mechanisms of action, drug indications and warnings. Use this skill to build curated SAR or QSAR datasets for a target, look compounds up by SMILES, InChIKey, name, or ChEMBL id, run similarity and substructure searches, and check what chemistry is already known…
- ClinicaltrialsK-DenseSearch the ClinicalTrials.gov registry through its version 2 REST API for interventional and observational studies, their phases, enrolment, endpoints, sponsors, and posted results. Use this skill to survey who is developing what against an indication, date a competitor's programme, read primary and secondary outcome measures, find eligibility criteria, and distinguish a study that completed…
- DegradersK-DenseWork on bifunctional degraders and molecular glues, where potency comes from a ternary complex rather than occupancy. Use this skill to apply the property rules that govern this beyond-rule-of-five space, reason about linker length, attachment vector and E3 ligase choice, prepare inputs for ternary complex structure prediction, and interpret degradation readouts — DC50, Dmax, cooperativity, and…
- DiffdockK-DenseDiffDock and DiffDock-L diffusion-based molecular docking. Use for blind protein-small-molecule pose prediction from a PDB file or sequence plus SMILES/SDF/MOL2, batch docking over a CSV of complexes, virtual screening triage, sampling multiple poses per complex, and reading the confidence score correctly.
- Generative DesignK-DenseGenerate and optimise novel small molecules with REINVENT 4 — de novo sampling from a chemical language model, scaffold decoration with LibInvent, fragment linking with LinkInvent, and similarity-constrained analogue generation with Mol2Mol.
- GlycoengineeringK-DenseAnalyze and engineer protein glycosylation. Scan sequences for canonical N-glycosylation sequons (N-X-S/T with X not proline, including overlapping sites), predict O-GalNAc hotspots, read glycan notation, and reach the curated external tooling (NetNGlyc, NetOGlyc, GlycoShield, GlycoWorkbench, GlyTouCan, GlyConnect).
- K-Dense-AI/drug-discovery-agent-skillsK-DenseCollectionAgent Skills for small-molecule and protein therapeutics: cheminformatics, molecular ML, docking and dynamics, protein design platforms, and target-discovery knowledge graphs.
- MedchemK-DenseMedicinal chemistry filters for compound triage. Apply drug-likeness rules (Lipinski rule of five, Veber, Oprea, CNS, lead-like, rule of three), structural alert catalogs (PAINS a/b/c, NIBR screening-deck severity, Brenk, BMS, Glaxo, Dundee, ChEMBL common alerts), ZINC-15 percentile complexity metrics (Bertz, SAscore, QED, Whitlock, Barone), chemical-group detection, Lilly demerits, and the…
- Molecular DynamicsK-DenseRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein and protein-ligand systems with PDBFixer, choose force fields and water models (AMBER14, CHARMM36m, ff19SB, GAFF2, TIP3P), solvate and add ions, run energy minimization, NVT/NPT equilibration and production MD on GPU, then analyze trajectories for RMSD, RMSF, radius of gyration, hydrogen bonds, native…
- MolfeatK-DenseMolecular featurization hub with one consistent interface over 100+ featurizers. Fingerprints (ECFP/Morgan, MACCS, atom pair, topological torsion, Avalon, RDKit, ERG), RDKit and Mordred descriptor sets, pharmacophore and 3D shape descriptors, scaffold keys, and pretrained embeddings (ChemBERTa, ChemGPT, MolT5, GIN, Graphormer) through a common transformer API with caching and parallelism.
- Open TargetsK-DenseQuery the Open Targets Platform GraphQL API for target-disease associations, genetic and clinical evidence, tractability and safety liabilities, target prioritisation metrics, known drugs and mechanisms of action, and disease ontology.
- OpenfdaK-DenseQuery the FDA's public openFDA APIs for post-market drug data — FAERS adverse-event reports, Drugs@FDA approval and submission history, Structured Product Labels including boxed warnings, the National Drug Code directory, recall enforcement reports, and drug shortages.
- Patent LandscapeK-DenseFind out whether a chemical series is already claimed, using SureChEMBL's patent-extracted compound corpus and, where a key is available, PatentsView for legal status and assignee history. Use this skill to trace a structure to the patent documents that disclose it, survey an assignee's filings around a target, and understand what the freedom-to-operate question requires that a structure search…
- PrimekgK-DenseQuery the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological relationships across genes and proteins, drugs, diseases, phenotypes, pathways, biological processes, exposures and anatomy.