PPI-GA: A Novel Clustering Algorithm to Identify Protein Complexes within Protein-Protein Interaction Networks Using Genetic Algorithm

• Published in: Complexity (New York, N.Y.) Vol. 2021; no. 1
• Main Authors: Shirmohammady, Naeem, Izadkhah, Habib, Isazadeh, Ayaz
• Format: Journal Article
• Language: English
• Published: Hoboken Hindawi 2021; John Wiley & Sons, Inc; Wiley
• Subjects: Accuracy; Bioinformatics; Clustering; Genetic algorithms; Proteins; Proteomics
• ISSN: 1076-2787; 1099-0526
• DOI: 10.1155/2021/2132516

Comprehensive analysis of proteins to evaluate their genetic diversity, study their differences, and respond to the tensions is the main subject of an interdisciplinary field of study called proteomics. The main objective of the proteomics is to detect and quantify proteins and study their post-translational modifications and interactions using protein chemistry, bioinformatics, and biology. Any disturbance in proteins interactive network can act as a source for biological disorders and various diseases such as Alzheimer and cancer. Most current computational methods for discovering protein complexes are usually based on specific topological characteristics of protein-protein networks (PPI). To identify the protein complexes, in this paper, we, first, present a new encoding method to represent solutions; we then propose a new clustering algorithm based on the genetic algorithm, named PPI-GA, employing a new multiobjective quality function. The proposed algorithm is evaluated on two gold standard and real-world datasets. The result achieved demonstrates that the proposed algorithm can detect important protein complexes, and it provides more accurate results compared with state-of-the-art protein complex identification algorithms.