PKU-YuanGroupOfficial·25 Agent Skills Included

OpenAI4S

Scientific research workflows for protein design, chemistry, and genomics

Runs end-to-end scientific research tasks: protein structure prediction, retrosynthesis planning, single-cell RNA analysis, literature review, and publication-grade figure composition. Eliminates manual pipeline wiring, unverified citations, and irreproducible results through persistent Python/R kernels, versioned artifacts, and evidence packages. Helps researchers complete GPU-heavy modeling, data audits, and report writing faster with built-in provenance and quality checks.

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npx skills add PKU-YuanGroup/OpenAI4S --all -g -y

Available:

Instructs the agent on the dual-loop architecture, routing JSON tool calls for orchestration and persistent Python/R kernels for scientific execution, plus testing and environment conventions.

All Skills in This Repository (25)

Pure Emerald Level Indicators

📦 In Repo

PKU-YuanGroup

figure-composer

Compose publication-quality multi-panel figures from narrative claims and data references.

using-model-endpoint

Infer from a registered model endpoint via its native HTTP API.

alphafold2

Predict protein structures for monomers and multimers with AlphaFold2.

solublempnn

Inverse-fold proteins with the SolubleMPNN model to optimize solubility.

esmfold2

Predict protein and nucleic acid structures using the ESMFold2 algorithm.

boltz

Predict protein, nucleic-acid, and small-molecule complex structures with Boltz-2.

remote-compute-nvidia

Orchestrate GPU computing jobs on NVIDIA NIM microservices.

remote-compute-ssh

Submit, monitor, and harvest compute jobs on SSH/SLURM hosts.

ligandmpnn

Design ligand-binding proteins with LigandMPNN and output PDB files.

pdf-explore

Navigate PDFs and extract structured content using pypdfium2 and Python.

scvi-tools

Automate single-cell RNA-seq batch integration, cell embedding, and differential expression with scVI and scANVI.

chai1

Predict protein, nucleic-acid, and small-molecule complex structures with Chai-1.

Official

Intermediate

Frequently Asked Questions

FAQPage Schema

How to install OpenAI4S?▼

Run `npx skills add PKU-YuanGroup/OpenAI4S --all -g -y` in your terminal to install all skills in this suite globally.

What scientific tasks can OpenAI4S handle?▼

It covers protein structure prediction and design, retrosynthesis and reaction analysis, single-cell RNA-seq workflows, literature reviews, dataset audits, and publication-grade figure generation.

Does OpenAI4S support GPU and remote compute?▼

Yes. It can dispatch GPU jobs to SSH/SLURM clusters or NVIDIA NIM services, with approval gates, job polling, and automatic output harvesting.

How does OpenAI4S prevent fabricated citations?▼

The literature-review skill verifies every DOI against Crossref and OpenAlex before writing, checks retraction flags, and grounds each claim in a retrieved source.

Can non-coders use OpenAI4S for research?▼

Yes. You describe the analysis in plain language and the agent runs the underlying Python/R kernels, models, and workflows for you.