Convergent algorithms for protein structural alignment |
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Authors: | Leandro Martínez Roberto Andreani José Mario Martínez |
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Affiliation: | (1) Institute of Chemistry, State University of Campinas, Campinas, SP, Brazil;(2) Department of Applied Mathematics, IMECC-UNICAMP, State University of Campinas, Campinas, SP, Brazil;(3) Department of Applied Mathematics, IMECC-UNICAMP, State University of Campinas, CP 6065, 13081-970 Campinas, SP, Brazil |
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Abstract: | Background Many algorithms exist for protein structural alignment, based on internal protein coordinates or on explicit superposition of the structures. These methods are usually successful for detecting structural similarities. However, current practical methods are seldom supported by convergence theories. In particular, although the goal of each algorithm is to maximize some scoring function, there is no practical method that theoretically guarantees score maximization. A practical algorithm with solid convergence properties would be useful for the refinement of protein folding maps, and for the development of new scores designed to be correlated with functional similarity. |
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