Protein Domain Boundary Predictions: A Structural Biology Perspective

Svetlana Kirillovaa, Suresh Kumara, Oliviero Carugo*, a, b
a Department of Biomolecular Structural Chemistry, Max F. Pertuz Laboratories, Vienna University, Campus Vienna, Biocenter 5, A-1030, Vienna
b Department of General Chemistry, Pavia University, Viale Taramelli 12, I-27100 Pavia, Italy

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© Kirillova et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Department of General Chemistry, Pavia University, Viale Taramelli 12, I-27100 Pavia, Italy; Tel: +43 1 4277 52208; E-mail:


One of the important fields to apply computational tools for domain boundaries prediction is structural biology. They can be used to design protein constructs that must be expressed in a stable and functional form and must produce diffraction-quality crystals. However, prediction of protein domain boundaries on the basis of amino acid sequences is still very problematical. In present study the performance of several computational approaches are compared. It is observed that the statistical significance of most of the predictions is rather poor. Nevertheless, when the right number of domains is correctly predicted, domain boundaries are predicted within very few residues from their real location. It can be concluded that prediction methods cannot be used yet as routine tools in structural biology, though some of them are rather promising.