A survey of computational methods in protein–protein interaction networks

Rasti, Saeid; Vogiatzis, Chrysafis

doi:10.1007/s10479-018-2956-2

Cited by 23 publications

(13 citation statements)

References 330 publications

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“…According to [32], one of the discrepancies for PPIN databases is due to high noise rates present in the outputs of the high‐throughput techniques used to obtain the interactions. This issue could be addressed by assigning probabilities to the edges which correspond to the probability that these interactions may or may not be present.…”

Section: Discussionmentioning

confidence: 99%

“…Systems biology involves the computational and mathematical analysis of large‐scale biological systems, such as the proteome. Complex network theory has been a staple of systems biology, and specifically the study of the proteome through the use of protein‐protein interaction networks: we refer the interested reader to a recent survey of computational techniques in PPINs [32]. Complex network theory has been so prominent that even in the early days of COVID‐19 spreading around the world, a network‐theoretic analysis of the main SARS‐COV‐2 protease and a comparison to its SARS‐COV‐1 counterpart had already been underway [10].…”

Section: Introductionmentioning

confidence: 99%

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Novel centrality metrics for studying essentiality in protein‐protein interaction networks based on group structures

Rasti

Vogiatzis

2021

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In this work, we introduce centrality metrics based on group structures, and we show their performance in estimating importance in protein-protein interaction networks (PPINs). The centrality metrics introduced are extensions of well-known nodal metrics. However, instead of focusing on a single node, we focus on that node and the set of nodes around it. Furthermore, we require the set of nodes to induce a specific pattern or structure. The structures investigated range from the "stricter" induced stars and cliques, to a "looser" definition of a representative structure. We derive the computational complexity of all metrics and provide mixed integer programming formulations; due to the problem complexity and the size of PPINs, using commercial solvers is not always viable. Hence, we propose a combinatorial branch-and-bound solution approach. We conclude by showing the effectiveness of the proposed metrics in identifying essential proteins in Helicobacter pylori and comparing them to nodal metrics.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Novel centrality metrics for studying essentiality in protein‐protein interaction networks based on group structures

Rasti

Vogiatzis

2021

Networks

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“…Several of the methods underlying clustering include variants of neighbourhood-based and random-walk based approaches, along with those based on network topology. Several reviews discuss the many approaches and applications of clustering [56] , [57] .…”

Section: Methods For Constructing and Contextualizing Ppinsmentioning

confidence: 99%

Construction and contextualization approaches for protein-protein interaction networks

Badkas

Landtsheer²,

Sauter³

2022

Computational and Structural Biotechnology Journal

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“…Comparison of both the clusters reveals that lesser number of proteins were involved with a higher number of interactions resulting into a dense network. Proteins in a dense network often forms functional modules that contributes to cellular processes (Rasti and Vogiatzis, 2019). Therefore knocking out of these proteins should result into a much lesser number of interactions which will lead to an overall loss of a number of functions of the proteins.…”

Section: Protein-protein Interaction Networkmentioning

confidence: 99%

In silico Metabolic Pathway Analysis Identifying Target Against Leishmaniasis – A Kinetic Modeling Approach

Bora

Jha

2020

Front. Genet.

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The protozoan Leishmania donovani, from trypanosomatids family is a deadly human pathogen responsible for causing Visceral Leishmaniasis. Unavailability of proper treatment in the developing countries has served as a major threat to the people. The absence of vaccines has made treatment possibilities to rely solely over chemotherapy. Also, reduced drug efficacy due to emerging resistant strains magnifies the threat. Despite years of formulations for an effective drug therapy, complexity of the disease is also unfortunately increasing. Absence of potential drug targets has worsened the scenario. Therefore exploring new therapeutic approach is a priority for the scientific community to combat the disease. One of the most reliable ways to alter the adversities of the infection is finding new biological targets for designing potential drugs. An era of computational biology allows identifying targets, assisting experimental studies. It includes sorting the parasite's metabolic pathways that pins out proteins essential for its survival. We have directed our study towards a computational methodology for determining targets against L. donovani from the "purine salvage" pathway. This is a mainstay pathway towards the maintenance of purine amounts in the parasitic pool of nutrients proving to be mandatory for its survival. This study represents an integration of metabolic pathway and Protein-Protein Interactions analysis. It consists of incorporating the available experimental data to the theoretical methods with a prospective to develop a kinetic model of Purine salvage pathway. Simulation data revealed the time course mechanism of the enzymes involved in the synthesis of the metabolites. Modeling of the metabolic pathway helped in marking of crucial enzymes. Additionally, the PPI analysis of the pathway assisted in building a static interaction network for the proteins. Topological analysis of the PPI network through centrality measures (MCC and Closeness) detected targets found common with Dynamic Modeling. Therefore our analysis reveals the enzymes ADSL (Adenylosuccinate lyase) and IMPDH (Inosine-5monophosphate dehydrogenase) to be important having a central role in the modeled network based on PPI and kinetic modeling techniques. Further the available three Frontiers in Genetics | www.frontiersin.org 1 March 2020 | Volume 11 | Article 179Bora and Jha Target Identification in L. donovani dimensional structure of the enzyme "ADSL" aided towards the search for potential inhibitors against the protein. Hence, the study presented the significance of integrating methods to identify key proteins which might be putative targets against the treatment of Visceral Leishmaniasis and their potential inhibitors.

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A survey of computational methods in protein–protein interaction networks

Cited by 23 publications

References 330 publications

Novel centrality metrics for studying essentiality in protein‐protein interaction networks based on group structures

Novel centrality metrics for studying essentiality in protein‐protein interaction networks based on group structures

Construction and contextualization approaches for protein-protein interaction networks

In silico Metabolic Pathway Analysis Identifying Target Against Leishmaniasis – A Kinetic Modeling Approach

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