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Most computational methods ignore the fact that proteins in a protein complex have a functional similarity and are co-localized and co-expressed at the same place and time, respectively. Meanwhile, the parameters of the current methods are specified by users, so these methods cannot effectively deal with different input PPI networks.<\/jats:p><\/jats:sec><jats:sec><jats:title>Result<\/jats:title><jats:p>To address these issues, this study proposes a new method called MP-AHSA to detect protein complexes with Multiple Properties (MP), and an Adaptation Harmony Search Algorithm is developed to optimize the parameters of the MP algorithm. First, a weighted PPI network is constructed using functional annotations, and multiple biological properties and the Markov cluster algorithm (MCL) are used to mine protein complex cores. Then, a fitness function is defined, and a protein complex forming strategy is designed to detect attachment proteins and form protein complexes. Next, a protein complex filtering strategy is formulated to filter out the protein complexes. Finally, an adaptation harmony search algorithm is developed to determine the MP algorithm\u2019s parameters automatically.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Experimental results show that the proposed MP-AHSA method outperforms 14 state-of-the-art methods for identifying protein complexes. Also, the functional enrichment analyses reveal that the protein complexes identified by the MP-AHSA algorithm have significant biological relevance.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-022-04923-4","type":"journal-article","created":{"date-parts":[[2022,10,7]],"date-time":"2022-10-07T08:04:15Z","timestamp":1665129855000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Detecting protein complexes with multiple properties by an adaptive harmony search algorithm"],"prefix":"10.1186","volume":"23","author":[{"given":"Rongquan","family":"Wang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caixia","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huimin","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,10,7]]},"reference":[{"issue":"6","key":"4923_CR1","doi-asserted-by":"publisher","first-page":"1000807","DOI":"10.1371\/journal.pcbi.1000807","volume":"6","author":"J De Las Rivas","year":"2010","unstructured":"De Las Rivas J, Fontanillo C. 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