Abstract
BackgroundProtein structure classification plays a central role in understanding the function of a protein molecule with respect to all known proteins in a structure database. With the rapid increase in the number of new protein structures, the need for automated and accurate methods for protein classification is increasingly important.ResultsIn this paper we present a unified framework for protein structure classification and identification of novel protein structures. The framework consists of a set of components for comparing, classifying, and clustering protein structures. These components allow us to accurately classify proteins into known folds, to detect new protein folds, and to provide a way of clustering the new folds. In our evaluation with SCOP 1.69, our method correctly classifies 86.0%, 87.7%, and 90.5% of new domains at family, superfamily, and fold levels. Furthermore, for protein domains that belong to new domain families, our method is able to produce clusters that closely correspond to the new families in SCOP 1.69. As a result, our method can also be used to suggest new classification groups that contain novel folds.ConclusionWe have developed a method called proCC for automatically classifying and clustering domains. The method is effective in classifying new domains and suggesting new domain families, and it is also very efficient. A web site offering access to proCC is freely available at
Highlights
Protein structure classification plays a central role in understanding the function of a protein molecule with respect to all known proteins in a structure database
Of the existing classification tools, both SGM [7] and SCOPmap [8] can be used to detect new classes, and as we show in this paper our method is much more effective compared to these two methods for new class detection
We employed the experimental strategies used in previous studies [8,9]: namely, domains in an older version of SCOP are used as the set of database domains with known class labels, and domains in a newer version of SCOP are used as the query set
Summary
Protein structure classification plays a central role in understanding the function of a protein molecule with respect to all known proteins in a structure database. Classification of protein domains based on their tertiary structure provides a valuable resource that can be used to understand protein function and evolutionary relationships [1]. While SCOP and CATH provide a valuable resource for biologists, these databases are updated only intermittently – for example, over the past three years, SCOP has been updated roughly every six months, and CATH has been updated annually. Updates to these databases require varying degrees of semi-automated methods and manual interpretation. The number of structures in PDB today is roughly double the number of structures in (page number not for citation purposes)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
