AbstractMultiple sequence alignments are a routine tool in protein fold recognition, but multiple structure alignments are computationally less cooperative. This work describes a method for protein sequence threading and sequence‐to‐structure alignments that uses multiple aligned structures, the aim being to improve models from protein threading calculations. Sequences are aligned into a field due to corresponding sites in homologous proteins. On the basis of a test set of more than 570 protein pairs, the procedure does improve alignment quality, although no more than averaging over sequences. For the force field tested, the benefit of structure averaging is smaller than that of adding sequence similarity terms or a contribution from secondary structure predictions. Although there is a significant improvement in the quality of sequence‐to‐structure alignments, this does not directly translate to an immediate improvement in fold recognition capability. Proteins 2002;47:496–505. © 2002 Wiley‐Liss, Inc.