Multiprot-a multiple protein structural alignment algorithm

Abstract

We present a fully automated highly efficient technique which detects the multiple structural alignments of protein structures. Our method, MultiProt, finds the common geometrical cores between the input molecules. To date, only few methods were developed to tackle the structural multiple alignment problem. Most of them require that all the input molecules be aligned, while our method does not require that all the input molecules participate in the alignment. Actually, it efficiently detects high scoring partial multiple alignments for all possible number of molecules from the input. To demonstrate the power of the presented method we provide a number of experimental results performed by the implemented program. Along with the known multiple alignments of protein structures, we present new multiple structural alignment results of protein families from the All beta proteins class in the SCOP classification.