Protein structure alignment using mean field annealing

Unraveling functional and ancestral relationships between proteins as well as structure prediction procedures require powerful protein alignment methods. This paper describes the use of fuzzy alignments when matching protein structures. The method use mean-field annealing optimization of fuzzy alignment variables, based on a cost expressed in terms of distances between aligned atoms and of gaps. The approach performs well when compared to other methods, requires modest CPU consumption, and is robust with respect to choice of iteration parameters for a wide range of proteins.