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ProFuMCell and ProModb: Web services for analyzing interaction-based functionally localized protein modules in a cell

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A Correction to this article was published on 19 April 2023

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Abstract

The modular organization of a cell which can be determined by its interaction network allows us to understand a mesh of cooperation among the functional modules. Therefore, cellular-level identification of functional modules aids in understanding the functional and structural characteristics of the biological network of a cell and also assists in determining or comprehending the evolutionary signal. We develop ProFuMCell that performs real-time Web scraping for generating clusters of the cellular level functional units of an organism. ProFuMCell constructs the Protein Locality Graphs and clusters the cellular level functional units of an organism by utilizing experimentally verified data from various online sources. Also, we develop ProModb, a database service that houses precomputed whole-cell protein-protein interaction network-based functional modules of an organism using ProFuMCell. Our Web service is entirely synchronized with the KEGG pathway database and allows users to generate spatially localized protein modules for any organism belonging to the KEGG genome using its real-time Web scraping characteristics. Hence, the server will host as many organisms as is maintained by the KEGG database. Our Web services provide the users a comprehensive and integrated tool for an efficient browsing and extraction of the spatial locality-based protein locality graph and the functional modules constructed by gathering experimental data from several interaction databases and pathway maps. We believe that our Web services will be beneficial in pharmacological research, where a novel research domain called modular pharmacology has initiated the study on the diagnosis, prevention, and treatment of deadly diseases using functional modules.

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Data availability

Publicly available ProFuMCell (https://cosmos.iitkgp.ac.in/ProFuMCell) and ProModb (https://cosmos.iitkgp.ac.in/ProModb) are free for all the users, and there is no login requirement.

Code availability

N/A

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Funding

This work was supported by the Open Competitive Grand Challenge Seed Grants (SGIGC) of Indian Institute of Technology Kharagpur (SRIC project code: WBC). B. D. is supported by an INSPIRE Fellowship (INSPIRE Code-IF150632) sponsored by the Department of Science and Technology, Government of India.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Indian Institute of Technology, Kharagpur, 721302, West Bengal, India

    Barnali Das & Pralay Mitra

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  1. Barnali Das
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  2. Pralay Mitra
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Contributions

B.D. and P.M. conceived the problem; B.D. designed and implemented the servers; B.D. analyzed the data; B.D. and P.M. wrote the paper.

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Correspondence to Pralay Mitra.

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The authors declare no competing interests.

Additional information

The original online version of this article was revised due to changes of method term in article title and body text.

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Das, B., Mitra, P. ProFuMCell and ProModb: Web services for analyzing interaction-based functionally localized protein modules in a cell. J Mol Model 28, 167 (2022). https://doi.org/10.1007/s00894-022-05133-8

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