In this paper a new Genetic Algorithm is proposed, called GAppi, which performs clustering in protein-protein interaction networks to identify protein complexes. The algorithm has been tested exhaustively with experimental datasets coming from online protein interaction databases and individual experiments and it has been compared with five other effective techniques in order to demonstrate its efficiency and superior performance. Results showed that GAppi produces feasible and very efficient solutions compared to other techniques. Except from that, due to its adaptive behavior, each time it is used it can satisfy different constraints, thus meeting the different needs of each user. Furthermore, a user friendly interface has been implemented that hosts the proposed algorithmic strategy.