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
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.
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.