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Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low‐resolution models
Author(s) -
de la Cruz Xavier,
Sillitoe Ian,
Orengo Christine
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10002
Subject(s) - low resolution , resolution (logic) , computer science , protein structure prediction , protein structure , protein structure database , data mining , high resolution , biological system , algorithm , artificial intelligence , chemistry , biology , genetics , biochemistry , remote sensing , sequence database , gene , geology
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 ≥5–7 Å, structure comparison methods were able to identify the fold of a protein in the top positions. Proteins 2002;46:72–84. © 2001 Wiley‐Liss, Inc.