https://github.com/rasbt/protein-recognition-index
Protein Recognition Index (PRI), measuring the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes
https://github.com/rasbt/protein-recognition-index
bioinformatics computational-biology protein-ligand-docking protein-ligand-interactions scoring-algorithm
Last synced: 5 months ago
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Protein Recognition Index (PRI), measuring the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes
- Host: GitHub
- URL: https://github.com/rasbt/protein-recognition-index
- Owner: rasbt
- License: apache-2.0
- Created: 2018-01-08T03:21:26.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2018-02-06T07:37:23.000Z (over 7 years ago)
- Last Synced: 2025-03-31T13:35:32.993Z (6 months ago)
- Topics: bioinformatics, computational-biology, protein-ligand-docking, protein-ligand-interactions, scoring-algorithm
- Language: Python
- Homepage: http://psa-lab.github.io/protein-recognition-index
- Size: 579 KB
- Stars: 8
- Watchers: 2
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Protein Recognition Index (PRI)
The Protein Recognition Index (PRI) measures the similarity between H-bonding features in a given complex (predicted or designed) and the characteristic H-bond trends from crystallographic complexes based on hydrogen-bond interactions idendified by [Hbind](https://github.com/psa-lab/Hbind) (software for rigorously defining intermolecular H-bonds by donor/acceptor chemistry and geometric constraints).
The PRI was developed, used, and described in detail in
- Raschka, Sebastian, Alex Wolf, Joseph Bemister‐Buffington, and Leslie A. Kuhn (2018) “Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes” Journal of Computer-Aided Molecular Design. *Journal of Computer-Aided Molecular Design* (accepted manuscript) [[biorxiv preprint](https://www.biorxiv.org/content/early/2018/02/05/260612)]
Documentation: https://psa-lab.github.io/protein-recognition-index
---
## Installation
No installation is required to execute the Protein Recognition Index software, which is available from the `code` subdirectory in this repository: [`./code/pri-score.py`](./code/pri-score.py). However, a current version of Python is required; we recommend [Python 3.6](https://www.python.org/downloads/release/python-360/) or greater.
In addition, running `pri-score.py` requires hydrogen-bond interaction tables as generated by [Hbind](http://psa-lab.github.io/Hbind). Hbind is freely available, and for more information on how to install and use it, please visit [http://psa-lab.github.io/Hbind](http://psa-lab.github.io/Hbind).
## Usage
The Protein Recognition Score software can be executed from the command line and takes an [Hbind](http://psa-lab.github.io/Hbind) interaction table as input, which lists the hydrogen-bond interactions between a protein and its ligand.
The following example illustrates how to compute the PRI score for the 1KPF [1KPF](https://www.rcsb.org/pdb/explore.do?structureId=1kpf) complex (PKCI-substrate analog) with its ligand `1KPF_AMP.mol2` (adenosine monophsophate). The structures are provided in the "[example_files/](./example_files)" subdirectory along with the generated Hbind interaction table.
---
[Interactions between an PKCI-substrate analog ([1KPF](https://www.rcsb.org/pdb/explore.do?structureId=1kpf)) with its ligand (adenosine monophsophate) via [HbindViz](https://github.com/rasbt/HbindViz) and [PyMOL](https://pymol.org); hydrogen atoms not shown]
---
To compute the PRI score, simply invoke the following command in your terminal:
python code/pri-score.py example_files/hbind_output.txt
The resulting output is shown below:
```
Protein Recognition Index, version 1.0.0
Documentation: http://psa-lab.github.io/protein-recognition-index
Raschka, Wolf, Bemister-Buffington, Kuhn (2018)
Protein Structure and Analysis Lab, MSU (http://kuhnlab.bmb.msu.edu)
Protein PRI: 252
Ligand PRI: 1584
PRI: 0.039
```
The Protein PRI (PRI-prot) and Ligand PRI (PRI-lig) scores are computed based on the hydrogen bond statistics across 136 non-homologous protein-ligand complexes as described in
- Raschka, Sebastian, Alex Wolf, Joseph Bemister‐Buffington, and Leslie A. Kuhn (2018) “Protein-ligand interfaces are polarized: discovery of a strong trend for intermolecular hydrogen bonds to favor donors on the protein side with implications for predicting and designing ligand complexes” Journal of Computer-Aided Molecular Design. *Journal of Computer-Aided Molecular Design* (accepted manuscript) [[biorxiv preprint](https://www.biorxiv.org/content/early/2018/02/05/260612)]
The PRI is then computed by standardizing the Protein and Ligand PRI scores and adding these, respectively:
Here, μ (mean) and σ (standard deviation) were derived from the 136 PRI-lig and PRI-prot scores computed from the 136 non-homologous complexes.