数据与复现蛋白结构与设计FreedomIntelligence/OpenClaw-Medical-Skills数据与复现
BI

bio-structural-biology-alphafold-predictions

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT).

OpenClawNanoClaw分析处理复现实验bio-structural-biology-alphafold-predictions🧬 bioinformatics (gptomics bio-* suite)bioinformatics — structural biology & cheminformaticsaccess

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-structural-biology-alphafold-predictions

维护者
FreedomIntelligence
许可
MIT
最近更新
2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

  • Python:requests.get(f'https://alphafold.ebi.ac.uk/files/AF-{uniprot}-F1-model_v4.pdb')。
  • Get AlphaFold predicted structure ,用于 my protein" → Download pre-computed AlphaFold structures by UniProt ID 、 assess prediction quality ,通过 per-residue pLDDT confidence scores. Python:requests.get(f'https://alphafold.ebi.ac.uk/files/AF-{uniprot}-F1-model_v4.pdb')。
  • Download 、 analyze AlphaFold predicted protein structures ,面向 AlphaFold Protein Structure Database。
  • Goal:Retrieve pre-computed AlphaFold protein structure predictions 、 assess prediction quality ,通过 pLDDT confidence scores。
  • Approach:Query AlphaFold Protein Structure Database API by UniProt accession to download PDB/CIF files,then extract per-residue pLDDT scores ,面向 B-factor columns to identify high-confidence 、 disordered regions。

原始文档

SKILL.md 摘录

File Types Available

Database version v4 (current as of 2025). The version number refers to the database release, not the AlphaFold model version.

FileURL PatternDescription
PDBAF-{id}-F1-model_v4.pdbStructure coordinates
mmCIFAF-{id}-F1-model_v4.cifStructure with metadata
PAE JSONAF-{id}-F1-predicted_aligned_error_v4.jsonPredicted aligned error

Extract from PDB B-factors

AlphaFold stores pLDDT scores in the B-factor column.

Confidence Interpretation

pLDDTConfidenceInterpretation
>90Very highHigh accuracy, can be used as experimental
70-90ConfidentGood backbone, may have sidechain errors
50-70LowCaution, may be disordered
<50Very lowLikely disordered or wrong

适用场景

  • 适合在predicted structures are needed ,用于 proteins without experimental structures,或 ,用于 confidence scores (pLDDT)时使用。

不适用场景

  • Do not rely on this catalog entry alone ,用于 installation 或 maintenance details。

上游相关技能

  • structural-biology/structure-io - Load and parse PDB/mmCIF files
  • structural-biology/geometric-analysis - RMSD, superimposition
  • database-access/uniprot-access - Get UniProt IDs for proteins
  • structural-biology/structure-navigation - Navigate structure hierarchy

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