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SkillsMP has collected 22 skills from BioTender-max/ProteinClaw. Open a skill to review its source and details.
Showing 22 of 22 collected skills.
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…
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…
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.
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…
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…
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…
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,…
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…
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…
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…
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)…
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…
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…
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…
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.…
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)…
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,…
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)…
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…
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…
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…
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…