title: Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models.
abstract: Predicting the three-dimensional structure of proteins is still one of the most challenging problems in molecular biology. Despite its difficulty, several investigators have started to produce consistently low-resolution predictions for small proteins. However, in most of these cases, the prediction accuracy is still too low to make them useful. In the present article, we address the problem of obtaining better-quality predictions, starting from low-resolution models. To this end, we have devised a new procedure that uses these models, together with structure comparison methods, to identify the structural family of the target protein. This would allow, in a second step not described in the present work, to refine the predictions using conserved features of the identified family. In our approach, the structure database is investigated using predictions, at different accuracy levels, for a given protein. As query structures, we used both low-resolution versions of the native structures, as well as different sets of low accuracy predictions. In general, we found that for predictions with a resolution of > or =5-7 A, structure comparison methods were able to identify the fold of a protein in the top positions.
authors.affiliation: Departmento de Bioquímica y Biología Molecular Facultad de Químicas; Universidad de Barcelona, Barcelona, Spain. xavier@husky.bq.ub.es
authors.forename: Xavier
authors.initials: X
authors.lastname: de la Cruz
authors.forename: Ian
authors.initials: I
authors.lastname: Sillitoe
authors.forename: Christine
authors.initials: C
authors.lastname: Orengo
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation