pdb-profiling 0.1.14a7

Profiling Protein Structures from Protein Data Bank and integrate various resources.🏄‍♂️

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
    • https://www.ebi.ac.uk/pdbe/api/doc/pdb.html
    • https://www.ebi.ac.uk/pdbe/api/doc/pisa.html
    • https://www.ebi.ac.uk/pdbe/api/doc/sifts.html
  • PDBe Graph API (Neo4j Graph DataBase)
    • https://www.ebi.ac.uk/pdbe/graph-api/pdbe_doc/
  • PDBe CoordinateServer API
    • https://www.ebi.ac.uk/pdbe/coordinates/index.html
    • https://cs.litemol.org/
  • ModelServer API
    • PDBe: https://www.ebi.ac.uk/pdbe/model-server/
    • RCSB: https://models.rcsb.org/
  • PDBe DensityServer API
    • https://ds.litemol.org/
  • PDBe VolumeServer API
    • https://www.ebi.ac.uk/pdbe/volume-server/
  • SWISS-MODEL Repository API
    • https://swissmodel.expasy.org/docs/smr_openapi
  • EBI Proteins API
    • https://www.ebi.ac.uk/proteins/api/doc/
  • UniProt API
    • https://www.uniprot.org/uploadlists/
    • https://www.uniprot.org/uniprot/*.fasta
  • Interactome3D API
    • https://interactome3d.irbbarcelona.org/
  • ModBase API (?)
  • Ensembl REST API
    • https://rest.ensembl.org/documentation
    • https://rest.ensembl.org/documentation/info/sequence_id
    • https://rest.ensembl.org/documentation/info/archive_id_get
  • Eutils API
    • https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
    • NOTE: currently only support minimum use
• Download data from PDB Archive against unexpected needs
  • wwPDB&RCSB: https://ftp.wwpdb.org/pub/pdb/data/structures/
  • EBI: http://ftp.ebi.ac.uk/pub/databases/pdb/data/structures/
  • wwPDB Versioned: http://ftp-versioned.wwpdb.org/pdb_versioned/data/entries/

Install

pip install pdb-profiling

Examples

See examples/...

1. Introduction
2. Batch
3. DisplayPDB
4. ...

Copyright Notice

This project is developed by Zefeng Zhu and hold by Minghui Group.

*Alternative Resources

• RCSB
  • Build Customize Tabular Reports of PDB Data
  • RCSB PDB Search API
    • Documentation for New and Improved APIs