pdb-profiling

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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

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.

Metadata

Release files for pdb-profiling 0.4.4

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pdb-profiling 0.4.4
File	Size	Uploaded
pdb_profiling-0.4.4.tar.gz	331.0 kB	Mar 30, 2023	Details

Release files / pdb_profiling-0.4.4.tar.gz

Download URL	pdb_profiling-0.4.4.tar.gz
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Uploaded via	`twine/3.7.1 importlib_metadata/6.0.0 pkginfo/1.9.6 requests/2.28.1 requests-toolbelt/0.9.1 tqdm/4.64.1 CPython/3.8.16`