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O SkillsMP coletou 22 skills de BioTender-max/ProteinClaw. Abra uma skill para revisar a origem e os detalhes.
Mostrando 22 de 22 skills coletadas.
Computational protein design toolkit. Use this skill group when: (1) Designing protein binders from scratch, (2) Predicting protein structures (Chai, Boltz, Protenix), (3) Sequence design with ProteinMPNN/LigandMPNN/SolubleMPNN, (4) Quality control and…
Idioma do texto original: inglês
Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen or BindCraft, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific…
Idioma do texto original: inglês
Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.
Idioma do texto original: inglês
Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand…
Idioma do texto original: inglês
All-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…
Idioma do texto original: inglês
Goal-oriented binder design campaign planning and health assessment. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) Assessing campaign health and pass rates, (4) Diagnosing why…
Idioma do texto original: inglês
Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic,…
Idioma do texto original: inglês
Structure prediction using Chai-1, a foundation model for molecular structure. Use this skill when: (1) Predicting protein-protein complex structures, (2) Validating designed binders, (3) Predicting protein-ligand complexes, (4) Using the Chai API for…
Idioma do texto original: inglês
ESM2 protein language model for embeddings and sequence scoring. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect…
Idioma do texto original: inglês
Structure 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…
Idioma do texto original: inglês
Antibody and nanobody CDR design using IgGM (generative model by TencentAI4S). Use this skill when: (1) Designing nanobody (VHH) CDR loops against a target, (2) Designing full antibody (heavy + light chain) CDRs, (3) Redesigning existing antibody CDRs, (4)…
Idioma do texto original: inglês
Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or BoltzGen outputs, (3) Comparing AF2/AF3/Boltz predictions, (4) Predicting binding…
Idioma do texto original: inglês
Ligand-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…
Idioma do texto original: inglês
VHH nanobody design using mBER (Manifold Binder Engineering and Refinement). Use this skill when: (1) Designing VHH nanobody CDRs against a target protein, (2) Have an existing VHH scaffold and want to redesign CDR1/CDR2/CDR3, (3) Optimizing a known VHH…
Idioma do texto original: inglês
Fetch 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.…
Idioma do texto original: inglês
End-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5)…
Idioma do texto original: inglês
Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines,…
Idioma do texto original: inglês
Design protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for generated backbones (e.g. from BindCraft), (2) Redesigning existing protein sequences, (3) Fixing specific residues while designing others, (4)…
Idioma do texto original: inglês
Structure prediction using Protenix, ByteDance's open-source PyTorch reproduction of AlphaFold 3. Use this skill when: (1) Predicting protein/DNA/RNA/ligand/ion complex structures, (2) Need AF3-level accuracy with open-source code, (3) MSA-free fast…
Idioma do texto original: inglês
First-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…
Idioma do texto original: inglês
Solubility-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…
Idioma do texto original: inglês
Access 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…
Idioma do texto original: inglês