Helix-bundle membrane protein fold templates

In the fold recognition approach to structure prediction, a sequence is tes ted for compatibility with an already known fold. For membrane proteins, ho wever, few folds have been determined experimentally. Here the feasibility of computing the vast majority of likely membrane protein folds is tested. The results indicate that conformation space can be effectively sampled for small numbers of helices. The vast majority of potential monomeric membran e protein structures can be represented by about 30-folds for three helices , but increases exponentially to about 1,500,000 folds for seven helices. T he generated folds could serve as templates for fold recognition or as star ting points for conformational searches that are well distributed throughou t conformation space.