Abstract Natural proteins quickly fold into a complicated three-dimensional structure. Evolutionary algorithms have been used to predict the native structure with the lowest energy conformation of the primary sequence of a given protein. Successful structure prediction requires a free energy function sufficiently close to the true potential for the native state, as well as a method for exploring the conformational space. Protein structure prediction is a challenging problem be- cause current potential functions have limited accuracy and the conformational space is vast. In this work, we show an innovative approach to the protein folding (PF) problem based on an hybrid Immune Algorithm (IMMALG) and a quasi-Newton method starting from a population of promising protein confor- mations created by the global optimizer DIRECT. The new method has been tested on Met-Enkephelin peptide, which is a paradigmatic example of multiple– minima problem, 1POLY, 1ROP and the three helix protein 1BDC. DIRECT produces an initial population of promising candidate solutions within a poten- tially optimal rectangle for the funnel landscape of the PF problem. Hence, IMMALG starts from a population of promising protein conformations created by the global optimizer DIRECT. The experimental results show that such a multistage approach is a competitive and effective search method in the con- formational search space of real proteins, in terms of solution quality and computational cost comparing the results of the current state-of-art algorithms. Keywords Clonal Selection Algorithms Æ DIRECT Æ Immune Algorithms Æ pattern search methods Æ protein folding Æ protein structure prediction Æ structural bioinformatics A. M. Anile Æ V. Cutello Æ G. Narzisi Æ G. Nicosia (&) Department of Mathematics and Computer Science, University of Catania, V.le A. Doria 6, 95125, Catania, Italy E-mail: nicosia@dmi.unict.it S. Spinella Department of Linguistics, University of Calabria, Ponte P. Bucci 17/B, 87036, Arcavata di Rende (CS), Italy 123 Nat Comput (2007) 6:55–72 DOI 10.1007/s11047-006-9027-3 ORIGINAL PAPER Determination of protein structure and dynamics combining immune algorithms and pattern search methods A. M. Anile Æ V. Cutello Æ G. Narzisi Æ G. Nicosia Æ S. Spinella Published online: 9 December 2006 Ó Springer Science+Business Media B.V. 2007