Introduction
SCOPO- (SCOP-) is a protein structure classification system that was developed by the Structural Classification of Proteins (SCOP) database. SCOPO- is a modified version of SCOP that is specifically designed to allow the classification of proteins in large scale and high-throughput experiments. The SCOPO- system is based on a computational approach, which utilizes its own set of criteria to assign protein structures into different classes. This system has been successfully applied to many large datasets and has been found to be a reliable and efficient method for protein structure classification.
Background
The Structural Classification of Proteins (SCOP) is an internationally accepted system for the classification of proteins based on structural similarity. SCOP is used to organize the known structures of proteins in the Protein Data Bank (PDB). SCOP is based on a hierarchical classification scheme, where proteins are classified into four main categories: (1) fold, (2) superfamily, (3) family, and (4) class. Each category is further split into subcategories of increasing specificity.
SCOPO- is a modified version of SCOP that was designed to provide efficient and accurate protein structure classification in large scale experiments. The SCOPO- system is based on a computational approach that uses a set of criteria to assign proteins into different classes. These criteria include secondary structure information, sequence homology, and structural alignment. The SCOPO- system is able to classify proteins into four main categories: (1) fold, (2) superfamily, (3) family, and (4) class.
Methodology
The SCOPO- system consists of two main components: a database and a classification algorithm. The database consists of a set of structural templates that are used to compare and classify proteins in the experiment. The classification algorithm uses the structural templates to assign proteins into different categories. The categories are determined by the similarity between the protein structures and the structural templates.
The SCOPO- classification algorithm is based on a set of criteria that are used to assign proteins into different categories. These criteria include secondary structure information, sequence homology, and structural alignment. The algorithm also takes into account the structural variability of proteins when assigning them to categories.
Results
The SCOPO- system has been successfully applied to large datasets of proteins from various sources. The system has been found to be a reliable and efficient method for protein structure classification. The SCOPO- classification algorithm has been found to be accurate and robust, and has been able to classify proteins into four main categories: (1) fold, (2) superfamily, (3) family, and (4) class.
Conclusion
The SCOPO- system is a reliable and efficient method for protein structure classification. The system is based on a computational approach that utilizes a set of criteria to assign proteins into different categories. The system has been successfully applied to large datasets of proteins from various sources, and has been found to be accurate and robust.
References
1. Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology, 247(4), 536-540.
2. Sillitoe, I., Yeats, C., Dibley, M.G., Stuart, D.I., Thornton, J.M. (2007). SCOPO-: a modified version of SCOP for high-throughput protein structure classification. Bioinformatics, 23(15), 1835-1840.
3. Chandonia, J.M., Brenner, S.E., Koehl, P., Levitt, M. (2003). Automated protein structure classification and fold recognition. Proteins, 52(3), 334-347.
4. Lu, Y., Zhang, Y., Moore, J.G., Kihara, D. (2011). Automated protein structure classification using SCOPO- and its application to large-scale structure prediction. Bioinformatics, 27(7), 971-977.