Profiling Protein Structures from Protein Data Bank and integrate various resources.
Project description
pdb-profiling
Profiling Protein Structures from Protein Data Bank and integrate various resources.
Goal
- Gather helpful/insightful indexes to evaluate a PDB structure's usefulness in:
- Entry level
- Assembly level
- Model level
- Entity level
- Chain level
- Residue level
- Define the representative set of protein structures:
- of a cluster with nearly identical sequences
- of UniProt Entry
- of UniProt Isoform
- or any other assigned structure dataset
- Provide interface for ID/residue mapping
- Apply mature and robust API to collect well-organized data
- PDBe REST API
- PDBe Graph API (Neo4j Graph DataBase)
- PDBe CoordinateServer API
- PDBe ModelServer API
- SWISS-MODEL Repository API
- EBI Proteins API
- UniProt API
- Interactome3D API
- ModBase API (?)
- Ensembl REST API
- https://rest.ensembl.org/documentation
- NOTE: currently only support https://rest.ensembl.org/documentation/info/sequence_id to retrieve ensembl sequences
- Eutils API
- https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
- NOTE: currently only support minimum use
- Download data from PDB Archive against unexpected needs
Install
pip install pdb-profiling
Examples
See examples/...
Copyright Notice
This project is developed by Zefeng Zhu and hold by Minghui Group.
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