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scientific-computing
124

bindcraft

End-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-qc. For tool selection guidance, use binder-design.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

alphafold

Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

uniprot

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 PDB structures. For structure retrieval, use pdb. For sequence design, use proteinmpnn.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

pdb

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. For sequence lookup, use uniprot. For binder design workflow, use binder-design.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

setup

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 up the environment, (5) biomodals directory is missing or tools aren't working.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

esm

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 prediction, (5) Analyzing sequence-function relationships. For structure prediction, use chai or boltz. For QC thresholds, use protein-qc.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

boltzgen

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 geometries, (5) Using YAML-based configuration. For backbone-only generation, use rfdiffusion. For sequence-only design, use proteinmpnn. For structure validation, use boltz.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

rfdiffusion

Generate 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 alphafold or chai. For QC thresholds, use protein-qc.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

chai

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 high-throughput prediction, (5) Need an alternative to AlphaFold2. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For ESM-based analysis, use esm.

adaptyvbio
adaptyvbio
research
open
scientific-computing
124

boltz

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 complexes, (5) Using local GPU resources. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For Chai prediction, use chai.

adaptyvbio
adaptyvbio
research
open
computational-chemistry
124

ipsae

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 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 chai or alphafold. For QC thresholds, use protein-qc.

adaptyvbio
adaptyvbio
research
open
computational-chemistry
124

binder-design

Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).

adaptyvbio
adaptyvbio
research
open
code-quality
124

code-review-quality

Conduct context-driven code reviews focusing on quality, testability, and maintainability. Use when reviewing code, providing feedback, or establishing review practices.

proffesor-for-testing
proffesor-for-testing
testing-security
open
automation-tools
124

refactoring-patterns

Apply safe refactoring patterns to improve code structure without changing behavior. Use when cleaning up code, reducing technical debt, or improving maintainability.

proffesor-for-testing
proffesor-for-testing
tools
open
debugging
124

sherlock-review

Evidence-based investigative code review using deductive reasoning to determine what actually happened versus what was claimed. Use when verifying implementation claims, investigating bugs, validating fixes, or conducting root cause analysis. Elementary approach to finding truth through systematic observation.

proffesor-for-testing
proffesor-for-testing
tools
open
health-fitness
124

bmi-bsa-calculator

Calculate Body Mass Index (BMI) and Body Surface Area (BSA) for clinical assessment, obesity screening, and chemotherapy dosing. Supports multiple BSA formulas (DuBois, Mosteller, Haycock), WHO weight classification, pediatric calculations, and metric/imperial input.

aipoch
aipoch
business
open
health-fitness
124

usmle-case-generator

Generate USMLE Step 1/2 style clinical cases with patient history, physical.

aipoch
aipoch
business
open
health-fitness
124

anatomy-quiz-master

Generate interactive anatomy quizzes for medical education with multiple.

aipoch
aipoch
business
open
real-estate-legal
124

prior-auth-letter-drafter

Generate professional prior authorization request letters for insurance companies with proper clinical justification and formatting.

aipoch
aipoch
business
open
real-estate-legal
124

dei-statement-drafter

Draft Diversity, Equity, and Inclusion statements for academic applications.

aipoch
aipoch
business
open
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