Antlion Optimization Algorithm for Pairwise Structural Alignment
Explore the application of the bi-objective Antlion Optimization Algorithm (BO-ALO) for improving pairwise protein structure alignment by minimizing RMSD score and maximizing TM score. The method outperforms existing approaches in benchmark datasets and biological significance evaluation.
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Presentation Transcript
Antlion optimization algorithm for pairwise structural alignment with bi-objective functions R. Ranjani Rani and D. Ramyachitra Neural Computing and Applications, 31(19), 2019, 3139 3146 Presenter: Feng-Yang Tsai Date:Jan. 7, 2019.
Abstract(1/2) This research work concentrates on the pairwise protein structure alignment of numerous protein structures. This is considered to be a problematic job which is an NP-hard problem. This work proposed a bi-objective-based antlion optimization algorithm (BO-ALO) which is aimed to improve the geometrical and evolutionary relationship among the protein structures. The bi-objective functions are the RMSD and TM scores which aim to minimize the RMSD score and maximize the TM score. The BO-ALO method has been compared with various widespread existing methods such as SPalignNS, UniAlign, DALI, MICAN, GANGSTA, DeepAlign, TM-align, CE, ant colony optimization and artificial bee colony optimization methods.
Abstract(2/2) The experiments were taken from the benchmark datasets, namely SCOPe and CATH. Also, the predicted alignments were compared with gold standard benchmark databases such as CDD, MALIDUP, MALISAM and HOMSTRAD. The outcomes of the proposed method have better bi- objective function scores and performance measures than other well-known existing approaches. This work also evaluates the proposed method with its biological significance of predicting the common gene ontology functions among the aligned protein structures.
Pareto-optimal solution: A non-dominated solution
Method: (a) Arbitrary random walks of ants (alignments):
Method: (b) Trapping in the antlions dump: (c) Sliding ants (alignments) toward antlions (residues):
Method: (d) Catching preys and reconstructing the trap: (e) Elitism:
