zongtingwei
- 20 skills
- 0 followers
- 9 hours ago last updated
- ▌ Pdb · zongtingwei bundleFetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, use uniprot. For binder design workflow, use binder-design-tool-selection.
- ▌ Ipsae · zongtingwei bundleBinder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or RFdiffusion outputs, (3) Comparing AF2/AF3/Boltz predictions, (4) Predicting binding success rates, (5) Need better ranking than ipTM or iPAE. For structure prediction, use chai1-structure-prediction or alphafold2-multimer. For QC thresholds, use protein-design-qc.
- ▌ Setup · zongtingwei bundleFirst-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.
- ▌ Uniprot · zongtingwei bundleAccess UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures. For structure retrieval, use pdb. For sequence design, use proteinmpnn.
- ▌ Boltzgen · zongtingwei bundleAll-atom protein design using BoltzGen diffusion model. Use this skill when: (1) Need side-chain aware design from the start, (2) Designing around small molecules or ligands, (3) Want all-atom diffusion (not just backbone), (4) Require precise binding geometries, (5) Using YAML-based configuration. For backbone-only generation, use rfdiffusion. For sequence-only design, use proteinmpnn. For structure validation, use boltz-structure-prediction.
- ▌ Foldseek · zongtingwei bundleStructure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai1-structure-prediction or boltz-structure-prediction.
- ▌ Bindcraft · zongtingwei bundleEnd-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-design-qc. For tool selection guidance, use binder-design-tool-selection.
- ▌ Ligandmpnn · zongtingwei bundleLigand-aware protein sequence design using LigandMPNN. Use this skill when: (1) Designing sequences around small molecules, (2) Enzyme active site design, (3) Ligand binding pocket optimization, (4) Metal coordination site design, (5) Cofactor binding proteins. For standard protein design, use proteinmpnn. For solubility optimization, use solublempnn.
- ▌ Proteinmpnn · zongtingwei bundleDesign protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing protein sequences, (3) Fixing specific residues while designing others, (4) Optimizing sequences for expression or stability, (5) Multi-state or negative design. For backbone generation, use rfdiffusion or bindcraft. For ligand-aware design, use ligandmpnn. For solubility optimization, use solublempnn.
- ▌ Rfdiffusion · zongtingwei bundleGenerate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers. For sequence design after backbone generation, use proteinmpnn. For structure validation, use alphafold2-multimer or chai1-structure-prediction. For QC thresholds, use protein-design-qc.
- ▌ Solublempnn · zongtingwei bundleSolubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation. For standard design, use proteinmpnn. For ligand-aware design, use ligandmpnn.
- ▌ Atac Seq · zongtingwei bundleATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.
- ▌ Chip Seq · zongtingwei bundleChIP-seq peak calling and downstream interpretation with MACS3, signal track export, annotation, motif analysis, and differential binding review.
- ▌ Proteomics · zongtingwei bundleMass spectrometry proteomics QC, quantification, comparative analysis, and export for DDA, DIA, and protein-level result tables.
- ▌ Cell Annotation · zongtingwei bundleAutomated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.
- ▌ Differential Expression · zongtingwei bundleBulk transcriptomics differential expression with count-aware modeling, design validation, contrast handling, thresholded exports, and publication-ready DE figures.
- ▌ Metagenomics · zongtingwei bundleShotgun metagenomics workflow with host-depletion-aware QC, taxonomic profiling, functional profiling, AMR follow-up, and reproducible community output tables.
- ▌ Phylogenetics · zongtingwei bundleWorkflow for multiple sequence alignment, tree inference, annotated tree visualization, and distance-based evolutionary comparison.
- ▌ Structural Biology · zongtingwei bundleStructure retrieval, confidence-aware AlphaFold DB usage, coordinate download, PAE and pLDDT interpretation, and structure-guided biological annotation.
- ▌ Scrna Preprocessing Clustering · zongtingwei bundleStandard scRNA-seq preprocessing and clustering with Scanpy. Use for QC, normalization, HVG selection, PCA, neighbor graph construction, UMAP, Leiden clustering, and export of an analysis-ready AnnData object.