%0 Journal Article
%T Preservation of protein clefts in comparative models
%A David Piedra
%A Sergi Lois
%A Xavier de la Cruz
%J BMC Structural Biology
%D 2008
%I BioMed Central
%R 10.1186/1472-6807-8-2
%X We studied how the largest cleft of a protein varies in comparative models. To this end, we analysed a set of 53507 homology models that cover the whole sequence identity range, with a special emphasis on medium and low similarities. More precisely we examined how cleft quality ¨C measured using six complementary parameters related to both global shape and local atomic environment, depends on the sequence identity between target and template proteins. In addition to this general analysis, we also explored the impact of a number of factors on cleft quality, and found that the relationship between quality and sequence identity varies depending on cleft rank amongst the set of protein clefts (when ordered according to size), and number of aligned residues.We have examined cleft quality in homology models at a range of seq.id. levels. Our results provide a detailed view of how quality is affected by distinct parameters and thus may help the user of comparative modelling to determine the final quality and applicability of his/her cleft models. In addition, the large variability in model quality that we observed within each sequence bin, with good models present even at low sequence identities (between 20% and 30%), indicates that properly developed identification methods could be used to recover good cleft models in this sequence range.In order to make full use of the growing amount of sequence information, in terms of increasing our knowledge of protein function, engineering new variants of known proteins, developing biomedical applications, etc, structural information is clearly required [1-6]. Indeed, one of the most important challenges in the post-genomics era is to fill the gap between the large number of known protein sequences and the still relatively small number of known structures [6-9]. Structural genomics projects have addressed this challenge and have led to the design and development of high-throughput production pipelines for structure determination [2,10-
%U http://www.biomedcentral.com/1472-6807/8/2