Comparison of non-sequential sets of protein residues |
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Institution: | 1. Department of Chemistry, Wayne State University, Detroit, MI 48202, United States;2. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, United States;1. Department of Physics, Kandaswami Kandar’s College, Velur, 638182, India;2. Department of Physics, Sri Shakthi Institute of Engineering and Technology, Coimbatore, 641062, India;3. CRM2, Lorraine University, CNRS, BP 70239, Vandoeuvre Les Nancy, Cedex, 54506, France;1. Department of CSE, MIST, Mirpur Cantonment, Dhaka 1216, Bangladesh;2. AℓEDA Group, Department of CSE, BUET, Dhaka 1215, Bangladesh |
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Abstract: | A methodology for performing sequence-free comparison of functional sites in protein structures is introduced. The method is based on a new notion of similarity among superimposed groups of amino acid residues that evaluates both geometry and physico-chemical properties. The method is specifically designed to handle disconnected and sparsely distributed sets of residues. A genetic algorithm is employed to find the superimposition of protein segments that maximizes their similarity. The method was evaluated by performing an all-to-all comparison on two separate sets of ligand-binding sites, comprising 47 protein-FAD (Flavin-Adenine Dinucleotide) and 64 protein-NAD (Nicotinamide-Adenine Dinucleotide) complexes, and comparing the results with those of an existing sequence-based structural alignment tool (TM-Align). The quality of the two methodologies is judged by the methods’ capacity to, among other, correctly predict the similarities in the protein-ligand contact patterns of each pair of binding sites. The results show that using a sequence-free method significantly improves over the sequence-based one, resulting in 23 significant binding-site homologies being detected by the new method but ignored by the sequence-based one. |
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Keywords: | Structural alignment Sequence-independent Structural similarity FAD NAD TM-SITE |
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