Construction of functional protein networks using domain profile associations

Jung Eun Shim, Insuk Lee

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Proteins are major functional molecules that physically and functionally interact to carry out cellular processes. The physical interactions are generally mediated by domain-level interactions. Thus, novel protein-protein interactions can be predicted using various computational methods based on domain-domain interactions, using resolved structures of protein complexes. Functional protein interactions can be inferred based on shared domains between proteins, since proteins involved in the same biological processes tend to harbor common domains. We recently developed a method of inferring functional interactions between proteins using associations between their domain compositions, which can be represented as domain profiles. Since the method requires only protein domain annotations, it can be easily applied to any species with a sequenced genome. Here, we describe in detail the method of generating domain profiles for proteins and measuring the association between them to infer functional interactions between proteins. We also demonstrate that domain profile association can be used to successfully construct a large-scale functional network of human proteins.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages35-44
Number of pages10
DOIs
Publication statusPublished - 2020 Jan 1

Publication series

NameMethods in Molecular Biology
Volume2074
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fingerprint

Proteins
Molecular Sequence Annotation
Biological Phenomena
Genome
Protein Domains

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Shim, J. E., & Lee, I. (2020). Construction of functional protein networks using domain profile associations. In Methods in Molecular Biology (pp. 35-44). (Methods in Molecular Biology; Vol. 2074). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9873-9_3
Shim, Jung Eun ; Lee, Insuk. / Construction of functional protein networks using domain profile associations. Methods in Molecular Biology. Humana Press Inc., 2020. pp. 35-44 (Methods in Molecular Biology).
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Shim, JE & Lee, I 2020, Construction of functional protein networks using domain profile associations. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 2074, Humana Press Inc., pp. 35-44. https://doi.org/10.1007/978-1-4939-9873-9_3

Construction of functional protein networks using domain profile associations. / Shim, Jung Eun; Lee, Insuk.

Methods in Molecular Biology. Humana Press Inc., 2020. p. 35-44 (Methods in Molecular Biology; Vol. 2074).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Shim JE, Lee I. Construction of functional protein networks using domain profile associations. In Methods in Molecular Biology. Humana Press Inc. 2020. p. 35-44. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9873-9_3