pdb-profiling

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

Features

• Collection: Implement various API to collect the well-organized metadata of PDB in real time.
• Integration: Provide a unified call for API-interface and return-data-form as well as subsequent data processing.
• Detection: Reorganize metadata to evaluate a PDB structure in Entry-Assembly/Model-Entity-Chain-Residue level and integrated with UniProt-KB.
• Interaction: Include UniProt Isoform Interaction in Asymmetric unit plus Biological Assembly level.
• Selection: Define the representative set of PDB structures in Monomeric|Homomeric|Heteromeric states.
• Mapping: Provide interface for both entry-identifier/accession-level and residue-level bidirectional mapping.

Install

Notice: require Python Environment >= 3.7, Platform Independent

Install by pip command.

*Before your Installation

• Make sure that your 64-bit machine is installed with 64-bit Python.
• To avoid some unexpected issues, you should upgrade your pip beforehand:

python -m pip install --upgrade pip

Official Installation

python -m pip install pdb-profiling

If you have already installed an older version of pdb-profiling, use the following command to install the latest version:

python -m pip install --upgrade pdb-profiling

Build From Source (optional, for non-windows environment)

python -m pip install cython
python -m pip install numpy
git clone https://github.com/NatureGeorge/pdb-profiling.git
python setup.py build_ext --inplace  # Need GCC or Other Compiler For C
python setup.py install              # or "sudo python setup.py install" or "python setup.py install --user"

Documentation

https://pdb-profiling.netlify.app/

Examples

Basic Usage

• Command Line Example
• Retrieve Bound Molecule Data From PDBe
• ...

Large-Scale-Example

• ExAC

Resources

• PDBe Entry-Based API
• PDBe Aggregated API (PDBe Graph API)
• PDBe ModelServer API
• SWISS-MODEL Repository API
• UniProt API
• EBI Proteins API
• RCSB Data API
• RCSB Search API
• Eutils API (minimum usage)
• ...

click here for more details

Related Resources

Using similar data resources but meant to achieve different goals.

Click to view

• RCSB: Build Customize Tabular Reports of PDB Data
• MolArt

Copyright Notice

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

License

The pdb_profiling.cython.py_qcprot module is derived from the cython wrapper contributed by Bernhard Thiel and is distributed under the terms of a BSD-3-Clause License. And it also contains the dependent C-code from http://theobald.brandeis.edu/QCP/ written by Pu Liu and Douglas Theobald (with slight modification by Bernhard Thiel) and is licensed under a BSD-3-Clause License.

The pdb_profiling is distributed under the terms of the MIT License.