Metadata-Version: 2.1
Name: pdb-profiling
Version: 0.1.16
Summary: Profiling Protein Structures from Protein Data Bank and integrate various resources.🏄‍♂️
Home-page: https://github.com/NatureGeorge/pdb-profiling
Author-email: 1730416009@stu.suda.edu.cn
Maintainer: ZeFeng Zhu
Maintainer-email: 1730416009@stu.suda.edu.cn
License: MIT
Description: # pdb-profiling
        
        [![Build](https://img.shields.io/travis/naturegeorge/pdb-profiling?style=for-the-badge&logo=travis)](https://github.com/naturegeorge/pdb-profiling)
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        ![cover](https://user-images.githubusercontent.com/43134199/95018149-58cfc200-0690-11eb-9e64-760faec5130f.png)
        
        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
        
        ```bash
        pip install pdb-profiling
        ```
        
        ## Examples
        
        See `examples/...`
        
        1. [Introduction](https://nbviewer.jupyter.org/github/NatureGeorge/pdb-profiling/blob/master/examples/Introduction.ipynb)
        2. [Batch](https://nbviewer.jupyter.org/github/NatureGeorge/pdb-profiling/blob/master/examples/Batch.ipynb)
        3. [DisplayPDB](https://nbviewer.jupyter.org/github/NatureGeorge/pdb-profiling/blob/master/examples/DisplayPDB.ipynb)
        3. ...
        
        ## Copyright Notice
        
        This project is developed by [Zefeng Zhu](https://github.com/NatureGeorge) and hold by [Minghui Group](https://lilab.jysw.suda.edu.cn/).
        
        ## *Alternative Resources
        
        * `RCSB`
          * [Build Customize Tabular Reports of PDB Data](https://www.rcsb.org/news?year=2020&article=5f6529e207302466657ec0e9&feature=true)
          * [RCSB PDB Search API](http://search.rcsb.org/)
            * [Documentation for New and Improved APIs](https://www.rcsb.org/news?year=2020&article=5f65165507302466657ec0e8&feature=true)
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.6.*
Description-Content-Type: text/markdown
