Protein complex prediction in large protein–protein interaction network
Due to high computational complexity, the detection of protein complexes in large protein–protein interaction (PPI) networks remains a challenging problem. Finding the actual protein complexes from a large PPI network requires a sophisticated algorithm. The protein complexes exhibit in densely conne...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-01-01
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| Series: | Informatics in Medicine Unlocked |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352914822000934 |
| _version_ | 1811235210801446912 |
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| author | Md. Shahidul Islam Md. Rafiqul Islam A.B.M. Shawkat Ali |
| author_facet | Md. Shahidul Islam Md. Rafiqul Islam A.B.M. Shawkat Ali |
| author_sort | Md. Shahidul Islam |
| collection | DOAJ |
| description | Due to high computational complexity, the detection of protein complexes in large protein–protein interaction (PPI) networks remains a challenging problem. Finding the actual protein complexes from a large PPI network requires a sophisticated algorithm. The protein complexes exhibit in densely connected sub-graphs in a PPI network. This paper presents a novel algorithm based on a metaheuristic method for protein complex prediction in large PPI networks. The algorithm mimics the density-based graph clustering method with biological heuristics to identify the protein complexes. The algorithm is enhanced by a local search algorithm and three repair operators. A new function has been developed for computing cluster density. The method was applied to the yeast and human protein interaction data and compared with the state-of-the-art algorithms. The comparisons demonstrate the best performance of the proposed algorithm in terms of accuracy and f-measure. |
| first_indexed | 2024-04-12T11:47:11Z |
| format | Article |
| id | doaj.art-6e0a6febe2914d43bbabbf761b0c7645 |
| institution | Directory Open Access Journal |
| issn | 2352-9148 |
| language | English |
| last_indexed | 2024-04-12T11:47:11Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Informatics in Medicine Unlocked |
| spelling | doaj.art-6e0a6febe2914d43bbabbf761b0c76452022-12-22T03:34:17ZengElsevierInformatics in Medicine Unlocked2352-91482022-01-0130100947Protein complex prediction in large protein–protein interaction networkMd. Shahidul Islam0Md. Rafiqul Islam1A.B.M. Shawkat Ali2University of Asia Pacific, Dhaka-1205, BangladeshKhulna University, Khulna-9208, Bangladesh; Corresponding author.Rajapore, Ghouradap, Jamalpur-2000, BangladeshDue to high computational complexity, the detection of protein complexes in large protein–protein interaction (PPI) networks remains a challenging problem. Finding the actual protein complexes from a large PPI network requires a sophisticated algorithm. The protein complexes exhibit in densely connected sub-graphs in a PPI network. This paper presents a novel algorithm based on a metaheuristic method for protein complex prediction in large PPI networks. The algorithm mimics the density-based graph clustering method with biological heuristics to identify the protein complexes. The algorithm is enhanced by a local search algorithm and three repair operators. A new function has been developed for computing cluster density. The method was applied to the yeast and human protein interaction data and compared with the state-of-the-art algorithms. The comparisons demonstrate the best performance of the proposed algorithm in terms of accuracy and f-measure.http://www.sciencedirect.com/science/article/pii/S2352914822000934Protein complex predictionChemical reaction optimizationProtein–protein interaction networkClustering |
| spellingShingle | Md. Shahidul Islam Md. Rafiqul Islam A.B.M. Shawkat Ali Protein complex prediction in large protein–protein interaction network Informatics in Medicine Unlocked Protein complex prediction Chemical reaction optimization Protein–protein interaction network Clustering |
| title | Protein complex prediction in large protein–protein interaction network |
| title_full | Protein complex prediction in large protein–protein interaction network |
| title_fullStr | Protein complex prediction in large protein–protein interaction network |
| title_full_unstemmed | Protein complex prediction in large protein–protein interaction network |
| title_short | Protein complex prediction in large protein–protein interaction network |
| title_sort | protein complex prediction in large protein protein interaction network |
| topic | Protein complex prediction Chemical reaction optimization Protein–protein interaction network Clustering |
| url | http://www.sciencedirect.com/science/article/pii/S2352914822000934 |
| work_keys_str_mv | AT mdshahidulislam proteincomplexpredictioninlargeproteinproteininteractionnetwork AT mdrafiqulislam proteincomplexpredictioninlargeproteinproteininteractionnetwork AT abmshawkatali proteincomplexpredictioninlargeproteinproteininteractionnetwork |