Protein structure and design

Retrieve and analyze AlphaFold predicted structures for a protein.

google-deepmind/science-skills

Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al.

JimLiu/science-skills

Validate protein designs using AlphaFold2 structure prediction.

adaptyvbio/protein-design-skills

Generate publication-quality molecular visualization images using PyMOL.

ChatMol/ChatMol

Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots from a name/sequence/PDB, co-design binder sequence+structure with reward-guided…

NVIDIA-BioNeMo/bionemo-agent-toolkit

End-to-end binder design using BindCraft hallucination. An agent skill from adaptyvbio/protein-design-skills.

adaptyvbio/protein-design-skills

Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.

K-Dense-AI/scientific-agent-skills

Guidance for choosing the right protein binder design tool. An agent skill from adaptyvbio/protein-design-skills.

adaptyvbio/protein-design-skills

Design and run computational protein and ligand workflows on a GPU: binder and enzyme design, de novo backbone generation, inverse folding and sequence redesign, structure prediction, protein-ligand…

locbp-uzh/biopipelines

All-atom protein design using BoltzGen diffusion model. An agent skill from adaptyvbio/protein-design-skills.

adaptyvbio/protein-design-skills

Structure prediction using Chai-1, a foundation model for molecular structure.

adaptyvbio/protein-design-skills

Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM skills.

NVIDIA-BioNeMo/bionemo-agent-toolkit

Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.

aiming-lab/AutoResearchClaw

End-to-end guidance for protein design pipelines. An agent skill from adaptyvbio/protein-design-skills.

adaptyvbio/protein-design-skills

Quality control metrics and filtering thresholds for protein design.

adaptyvbio/protein-design-skills

Best practices for protein structure refinement and validation in Coot.

pemsley/coot

Design protein sequences using ProteinMPNN inverse folding. An agent skill from adaptyvbio/protein-design-skills.

adaptyvbio/protein-design-skills

Query public biology databases and APIs including UniProt, RCSB PDB, AlphaFold DB, ClinVar, dbSNP, gnomAD, Ensembl, GEO, InterPro, KEGG, OpenTargets, Reactome, and STRING.

DrugClaw/DrugClaw

Identify and rank ligandable pockets on a protein structure or model using geometry (fpocket) or an ML predictor (P2Rank).

learningmatter-mit/AtomisticSkills

CLI/Python toolkit for rapid bioinformatics queries. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

Prepare, launch, monitor, and summarize the real RFdiffusion to ProteinMPNN to Protenix antibody pipeline on a local or remote ScienceDiscovery Runner with sandboxed Ascend NPUs.

openJiuwen-ai/sciencediscovery

Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation.

adaptyvbio/protein-design-skills

Cloud laboratory platform for automated protein testing and validation.

davila7/claude-code-templates

Access AlphaFold's 200M+ AI-predicted protein structures. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

End-to-end Proteina-Complexa design pipeline driver. An agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit.

NVIDIA-BioNeMo/bionemo-agent-toolkit

Visualize, analyze, and render protein and molecular structures using PyMOL.

google-deepmind/science-skills

Access protein metadata, function, taxonomy, and sequences across UniProtKB, UniParc, and UniRef.

google-deepmind/science-skills

Access RCSB PDB for 3D protein/nucleic acid structures. An agent skill from davila7/claude-code-templates.

davila7/claude-code-templates

A skill your agent uses when working with scientific research tools and workflows across bioinformatics, cheminformatics, genomics, structural biology, proteomics, and drug discovery.

ynulihao/AgentSkillOS

Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API.

google-deepmind/science-skills

Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor.

adaptyvbio/protein-design-skills

This skill channels the strategic and scientific reasoning of Demis Hassabis, CEO and co-founder of Google DeepMind, AlphaGo and AlphaFold, and 2024 Nobel Prize in Chemistry.

K-Dense-AI/mimeo

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and…

davila7/claude-code-templates

Guidance for cell-free protein synthesis (CFPS) optimization.

adaptyvbio/protein-design-skills

Query InterPro for protein family, domain, and functional site annotations.

LeonChaoX/qinyan-academic-skills

Generate de novo protein backbones with RFdiffusion for protein-target binders, hotspot-conditioned interfaces, motif scaffolding, partial diffusion, or symmetric assemblies.

PKU-YuanGroup/OpenAI4S

Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog.

K-Dense-AI/scientific-agent-skills

Provides access to a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required.

K-Dense-AI/scientific-agent-skills

Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al.

JimLiu/science-skills

Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab).

JimLiu/science-skills

Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al.

JimLiu/science-skills

Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al.

JimLiu/science-skills

Binder design ranking using ipSAE (interprotein Score from Aligned Errors).

adaptyvbio/protein-design-skills

Ligand-aware protein sequence design using LigandMPNN. An agent skill from adaptyvbio/protein-design-skills.

adaptyvbio/protein-design-skills

Fetch and analyze protein structures from RCSB PDB. An agent skill from adaptyvbio/protein-design-skills.

adaptyvbio/protein-design-skills

Solubility-optimized protein sequence design using SolubleMPNN.

adaptyvbio/protein-design-skills

A skill your agent uses for AlphaFold 3 input preparation, prediction command planning, output interpretation, and Python API inspection.

VectorSpaceLab/AREX-Skill

Runs and analyzes molecular dynamics simulations with OpenMM and MDAnalysis.

K-Dense-AI/scientific-agent-skills