Run any Skill in Manus with one click

foldseek

Stars11

Forks0

UpdatedMarch 4, 2026 at 07:22

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 structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.

Installation

Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.

Run Skill in Manus

Source

BioTender-max

BioTender-max/ProteinClaw

View GitHub Repository View Creator Repositories

Download

Run Skill in Manus

Related occupationsSOC

Based on SOC occupation classification

Biochemists and BiophysicistsLife, Physical, and Social Science Occupations·SOC 19-1021

SKILL.md

readonly

name	foldseek
description	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 structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.
license	MIT
category	utilities
tags	["search","structure","database","similarity"]
source	https://github.com/adaptyvbio/protein-design-skills

Foldseek Structure Search

Prerequisites

Requirement	Minimum	Recommended
RAM	8GB	16GB
Disk	10GB	50GB (local databases)

No GPU required.

How to run

Option 1: Web Server (Quick, rate-limited)

curl -X POST "https://search.foldseek.com/api/ticket" \
  -F "q=@query.pdb" \
  -F "database[]=afdb50" \
  -F "database[]=pdb100"

Option 2: Local installation

conda install -c conda-forge -c bioconda foldseek

# Search PDB
foldseek easy-search query.pdb /path/to/pdb100 results.m8 tmp/

# Search AlphaFold DB
foldseek easy-search query.pdb /path/to/afdb50 results.m8 tmp/

Key Parameters

Parameter	Default	Description
`--min-seq-id`	0.0	Minimum sequence identity
`-e`	0.001	E-value threshold
`--alignment-type`	2	0=3Di, 1=TM, 2=3Di+AA

Databases

Database	Description	Size
`pdb100`	PDB clustered at 100%	~200K structures
`afdb50`	AlphaFold DB at 50%	~67M structures
`swissprot`	SwissProt structures	~500K structures

Common Use Cases

Novelty check

foldseek easy-search design.pdb afdb50 novelty.m8 tmp/
# Novel if: top hit identity < 30%

Find similar natural structures

foldseek easy-search design.pdb pdb100 similar_natural.m8 tmp/

Scaffold search for motif grafting

foldseek easy-search motif.pdb pdb100 scaffolds.m8 tmp/ \
  --min-seq-id 0.0 -e 10

Decision Tree

Searching by?
├─ 3D structure → Foldseek ✓
├─ Sequence → Use BLAST (uniprot skill)
└─ Both → Run both, compare results

Troubleshooting

Error	Cause	Fix
No hits	Too strict cutoff	Lower e-value, try larger database
`Database not found`	Wrong path	Check database location
Out of memory	Large database	Use web server

Next: Download hits with pdb skill → use for scaffold design.

More from this repository

same repository

protein-design

BioTender-max/ProteinClaw

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 filtering of protein designs, (5) Planning and managing binder design campaigns, (6) Experimental characterization (SPR, BLI, cell-free expression), (7) Searching protein databases (PDB, UniProt, AFDB), (8) Antibody/nanobody design (IgGM, mBER). This is the top-level index. Sub-skills handle specific tools.

2026-03-0411

binder-design

BioTender-max/ProteinClaw

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 target types.

2026-03-0411

binding-characterization

BioTender-max/ProteinClaw

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.

2026-03-0411

boltz

BioTender-max/ProteinClaw

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.

2026-03-0411

boltzgen

BioTender-max/ProteinClaw

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 sequence-only design, use proteinmpnn. For structure validation, use boltz.

2026-03-0411

campaign-manager

BioTender-max/ProteinClaw

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 designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target. This skill orchestrates the other protein design tools.

2026-03-0411

name	foldseek
description	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 structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.
license	MIT
category	utilities
tags	["search","structure","database","similarity"]
source	https://github.com/adaptyvbio/protein-design-skills

Foldseek Structure Search

Prerequisites

Requirement	Minimum	Recommended
RAM	8GB	16GB
Disk	10GB	50GB (local databases)

No GPU required.

How to run

Option 1: Web Server (Quick, rate-limited)

curl -X POST "https://search.foldseek.com/api/ticket" \
  -F "q=@query.pdb" \
  -F "database[]=afdb50" \
  -F "database[]=pdb100"

Option 2: Local installation

conda install -c conda-forge -c bioconda foldseek

# Search PDB
foldseek easy-search query.pdb /path/to/pdb100 results.m8 tmp/

# Search AlphaFold DB
foldseek easy-search query.pdb /path/to/afdb50 results.m8 tmp/

Key Parameters

Parameter	Default	Description
`--min-seq-id`	0.0	Minimum sequence identity
`-e`	0.001	E-value threshold
`--alignment-type`	2	0=3Di, 1=TM, 2=3Di+AA

Databases

Database	Description	Size
`pdb100`	PDB clustered at 100%	~200K structures
`afdb50`	AlphaFold DB at 50%	~67M structures
`swissprot`	SwissProt structures	~500K structures

Common Use Cases

Novelty check

foldseek easy-search design.pdb afdb50 novelty.m8 tmp/
# Novel if: top hit identity < 30%

Find similar natural structures

foldseek easy-search design.pdb pdb100 similar_natural.m8 tmp/

Scaffold search for motif grafting

foldseek easy-search motif.pdb pdb100 scaffolds.m8 tmp/ \
  --min-seq-id 0.0 -e 10

Decision Tree

Searching by?
├─ 3D structure → Foldseek ✓
├─ Sequence → Use BLAST (uniprot skill)
└─ Both → Run both, compare results

Troubleshooting

Error	Cause	Fix
No hits	Too strict cutoff	Lower e-value, try larger database
`Database not found`	Wrong path	Check database location
Out of memory	Large database	Use web server

Next: Download hits with pdb skill → use for scaffold design.