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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 (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]

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. However, a current version of Python is required; we recommend Python 3.6 or greater.

In addition, running pri-score.py requires hydrogen-bond interaction tables as generated by Hbind. Hbind is freely available, and for more information on how to install and use it, please visit http://psa-lab.github.io/Hbind.

Usage

The Protein Recognition Score software can be executed from the command line and takes an 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 complex (PKCI-substrate analog) with its ligand 1KPF_AMP.mol2 (adenosine monophsophate). The structures are provided in the "example_files/" subdirectory along with the generated Hbind interaction table.

[Interactions between an PKCI-substrate analog (1KPF) with its ligand (adenosine monophsophate) via HbindViz and PyMOL; 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]

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.