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.
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 >= 3.6, 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
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
Resources
- PDBe Entry-Based API
- PDBe Aggregated API (PDBe Graph API)
- PDBe ModelServer API
- SWISS-MODEL Repository API
- UniProt API
- EBI Proteins API
- Interactome3D API
- RCSB Data API
- RCSB Search API
- ...
click here for more details
Related Resources
Using similar data resources but meant to achieve different goals.
Click to view
Copyright Notice
This project is developed by Zefeng Zhu and hold by Minghui Group.
Project details
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Source Distribution
pdb_profiling-0.3.2a1.tar.gz
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