All authors
Claude Skills by ssinder
github.com/ssinder17 skills0 installs0 views
- Alphafold DbDownloads predicted protein structures from the EBI AlphaFold Database API and exports per-protein prediction metadata. Resolves the current PDB/CIF download URL from the API instead of hard-coding a model version, supports batch accession lists, resumable downloads, pLDDT-based quality filtering before spending bandwidth, and validates response content types so HTML error pages are never mistaken for structure files. This skill should be used when fetching AlphaFold models, retrieving predic...Votes: 0GitHub stars: 75
- Bio Database FetchFetches compound properties and species taxonomy from the official PubChem PUG-REST and NCBI Taxonomy APIs. Retrieves molecular formula, weight, SMILES, InChI, InChIKey, IUPAC name, XLogP, TPSA and CAS numbers for a batch of PubChem CIDs, and full lineage classification (domain through species) for a batch of NCBI Taxonomy IDs. Supports batched queries (100 IDs per request), CSV/JSON export, and requires a contact email as the NCBI usage policy mandates. This skill should be used when looking...Votes: 0GitHub stars: 75
- Bioproject SearchRetrieves NCBI BioProject metadata — title, description, organism, submitter and release dates — for a batch of BioProject accessions, using the official NCBI E-utilities API rather than scraping the BioProject web pages. Supports keyword filtering over titles and descriptions, CSV/JSON export, and requires a contact email as the NCBI usage policy mandates. This skill should be used when looking up what a BioProject or PRJNA/PRD accession contains, retrieving sequencing project descriptions, ...Votes: 0GitHub stars: 75
- Bulk RnaseqThis skill should be used when running bulk RNA-seq differential expression analysis: FastQC/trimming, Salmon quantification, counts matrix construction, DESeq2 statistics, GO/KEGG enrichment and publication figures. 用于 bulk 转录组（RNA-seq）差异表达分析全流程。Votes: 0GitHub stars: 75
- Ena DownloadDownloads RNA-seq and other sequencing FASTQ data from the ENA (European Nucleotide Archive) Portal API and exports run-level metadata. Resolves download URLs and file sizes from the structured API rather than scraping archive web pages, supports batch accession lists, HTTP Range resume for interrupted transfers, and MD5 verification against the checksums ENA publishes. This skill should be used when fetching raw sequencing reads by SRA/ERR/DRR accession, retrieving FASTQ files for an RNA-seq...Votes: 0GitHub stars: 75
- Literature SearchThis skill should be used when mining academic literature from PubMed, OpenAlex or Semantic Scholar — searching papers by topic or keywords, deduplicating multi-source results, filtering by relevance or citation count, enriching missing abstracts, and exporting RIS, BibTeX or GB/T 7714 citations. 用于多源学术文献检索、去重、相关性筛选、摘要富集与参考文献格式导出的场景。Votes: 0GitHub stars: 75
- Ml Peptide GenerationGenerates candidate binder peptides for a target protein using the PepMLM-650M masked language model — appends <mask> tokens to the target sequence and samples amino acids at each position, with illegal residues (X, B, Z) excluded from the sampling candidates. Reports pseudo-perplexity for each candidate, supports reproducible generation via an explicit random seed, and provides offline filtering and parameter-sweep analysis that needs no GPU. This skill should be used when designing peptides...Votes: 0GitHub stars: 75
- Molecular DynamicsAnalyses molecular-dynamics trajectories with a self-contained pure-numpy DCD and PDB trajectory parser plus built-in Kabsch-Sander alignment, SVD-based PCA, hierarchical clustering of RMSD matrices, geometric hydrogen-bond detection, RMSF, radius of gyration, Ramachandran analysis, inter-chain contacts and Shrake-Rupley SASA. This skill should be used when trajectory RMSD or RMSF, PCA, conformational clustering, hydrogen-bond occupancy, Ramachandran plots or solvent-accessible surface analys...Votes: 0GitHub stars: 75
- Paper Fulltext ExtractThis skill should be used when extracting structured full text from scientific PDF papers — converting PDFs to TEI XML via a local GROBID service, parsing titles, authors, abstracts, keywords, section trees, figures and references into JSON, Markdown or HTML, building a searchable corpus index across many papers, and pulling the first sentences of each Introduction paragraph for rapid paper triage. 用于科研 PDF 全文结构化抽取、TEI 解析、文献语料全文检索与引言精读的场景。Votes: 0GitHub stars: 75
- Peptide DesignThis skill should be used when analyzing or designing antimicrobial peptides — computing physicochemical properties such as molecular weight, isoelectric point, Kyte-Doolittle hydrophobicity and instability index, classifying peptides as antimicrobial or non-antimicrobial from GO terms and sequence features, deduplicating peptide libraries by clustering, and exporting FASTA or CSV. 用于多肽理化性质计算、抗菌肽判别、序列聚类去冗余与导出的场景。Votes: 0GitHub stars: 75
- Protein Docking HdockSubmits protein-protein docking jobs to the HDOCK server and retrieves the resulting Docking Score, Confidence Score, ligand RMSD and ranked complex models. Uses plain HTTP form submission against the HDOCK server rather than browser automation, supports PDB files, PDB ID:ChainID references and FASTA sequences for both receptor and ligand, records submitted jobs to a CSV so results can be collected later, and can poll for completion. This skill should be used when running protein-protein comp...Votes: 0GitHub stars: 75
- Protein Docking LightdockRuns LightDock protein-protein docking locally by driving the lightdock3_setup.py and lightdock3.py executables, then extracts the best docked complex. Parses the GSO swarm output files with the correct field semantics (glowworm id is the line number, not the LigID column), selects the latest gso_<step>.out by numeric step rather than dictionary order, and generates conformations from the origin-shifted structures that the setup stage produced so the receptor and ligand stay in a consistent c...Votes: 0GitHub stars: 75
- Protein InteractionsAnalyzes protein-ligand and protein-protein interactions from PLIP XML reports and AlphaFold model packages using a self-contained standard-library XML parser: extracts residue-level salt bridges, hydrogen bonds, hydrophobic, pi-stacking, water bridges, halogen bonds and metal complexes, ranks hotspot residues, and emits Mermaid network graphs plus PyMOL annotation scripts. This skill should be used when interaction detection, hotspot ranking, PLIP report parsing, interaction network visualis...Votes: 0GitHub stars: 75
- Protein StructureAnalyzes protein structures from PDB files: parses ATOM/HETATM records with a dependency-free pure-Python parser, computes radius of gyration, gyration tensor and dipole moments, assigns secondary structure via DSSP or a built-in Kabsch-Sander hydrogen-bond implementation, and optionally retrieves UniProt metadata. This skill should be used when secondary structure assignment, Rg, shape analysis, DSSP, PDB parsing or protein structure annotation is requested.Votes: 0GitHub stars: 75
- Pymol Structure VisualizationThis skill should be used when analyzing inter-chain contacts in protein structures — computing residue-level contact geometry from PDB files with a uniform-grid spatial index, classifying each contact into hydrogen bonds, salt bridges, hydrophobic contacts, pi-pi stacking and cation-pi interactions using residue chemistry, identifying hotspot residues, and exporting CSV/JSON results together with Mermaid interaction networks and ready-to-run PyMOL visualization scripts. 用于 PDB 链间残基接触分析、结合界面热...Votes: 0GitHub stars: 75
- Scientific FiguresThis skill should be used when generating publication-ready scientific figures — ROC curves, confusion matrix heatmaps, docking binding-energy heatmaps, pLDDT confidence histograms, SHAP summary beeswarms, class distribution charts and other chart types with a unified journal-grade visual style. 用于生成顶刊级出版图表（ROC 曲线、混淆矩阵、热图、pLDDT 分布、SHAP 摘要等）的场景。Votes: 0GitHub stars: 75
- Single Cell RnaseqThis skill should be used when running single-cell RNA-seq analysis: reading 10x/AnnData matrices, QC filtering, normalization, HVG selection, PCA, clustering, UMAP/t-SNE and cell type annotation. 用于单细胞转录组（scRNA-seq）质控、降维、聚类与细胞注释全流程。Votes: 0GitHub stars: 75