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PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein–protein interfaces

  • Published:
Journal of Structural and Functional Genomics

Abstract

Residues in a protein–protein interface that are important for forming and stabilizing the interaction can usually be identified by looking at patterns of evolutionary conservation in groups of homologous proteins and also by the computational identification of binding hotspots. The PRICE (PRotein Interface Conservation and Energetics) server takes the coordinates of a protein–protein complex, dissects the interface into core and rim regions, and calculates (1) the degree of conservation (measured as the sequence entropy), as well as (2) the change in free energy of binding (∆∆G, due to alanine scanning mutagenesis) of interface residues. Results are displayed as color-coded plots and also made available for download. This enables the computational identification of binding hot spots, based on which further experiments can be designed. The method will aid in protein functional prediction by correct assignment of hot regions involved in binding. Consideration of sequence entropies for residues with large ∆∆G values may provide an indication of the biological relevance of the interface. Finally, the results obtained on a test set of alanine mutants has been compared to those obtained using other servers/methods. The PRICE server is a web application available at http://www.boseinst.ernet.in/resources/bioinfo/stag.html.

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Acknowledgments

The work was funded by the Department of Biotechnology, India. We thank Ms. Paramita Ghosh for her help in the implementation of the program.

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Authors and Affiliations

  1. Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700 054, India

    Mainak Guharoy, Arumay Pal & Pinak Chakrabarti

  2. Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700 054, India

    Maitrayee Dasgupta & Pinak Chakrabarti

Authors
  1. Mainak Guharoy
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  2. Arumay Pal
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  3. Maitrayee Dasgupta
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  4. Pinak Chakrabarti
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Corresponding author

Correspondence to Pinak Chakrabarti.

Additional information

Mainak Guharoy and Arumay Pal have contributed equally.

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Guharoy, M., Pal, A., Dasgupta, M. et al. PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein–protein interfaces. J Struct Funct Genomics 12, 33–41 (2011). https://doi.org/10.1007/s10969-011-9108-0

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  • DOI: https://doi.org/10.1007/s10969-011-9108-0

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