PMC:5056897 / 11086-12729 JSONTXT

{"project":"2_test","denotations":[{"id":"27729842-23203873-44840783","span":{"begin":244,"end":246},"obj":"23203873"},{"id":"27729842-10592240-44840784","span":{"begin":262,"end":264},"obj":"10592240"},{"id":"27729842-23193289-44840785","span":{"begin":276,"end":278},"obj":"23193289"},{"id":"27729842-14681378-44840786","span":{"begin":287,"end":289},"obj":"14681378"},{"id":"27729842-12368255-44840787","span":{"begin":299,"end":301},"obj":"12368255"},{"id":"27729842-12824396-44840788","span":{"begin":313,"end":315},"obj":"12824396"},{"id":"27729842-22121228-44840789","span":{"begin":332,"end":334},"obj":"22121228"}],"text":"Classification and domain assignment\nProtein classification and domain assignment using sequence similarity search may give ample evidence for function prediction of the HPs. We have used an array of databases and retrieval tools such as CATH [50], SUPERFAMILY [51], PANTHER [52], Pfam [53], CDART [54], SVMProt [55], and ProtoNet [56] for the classification of the HPs. CATH provides the classification of Protein Data Bank (PDB) protein structure repository. CATH v4.0 release contains 235,858 domains, 2,738 superfamily and 69,058 annotated PDBs. SUPERFAMILY database provides structure and functional annotation of proteins based on HMM using SCOP classification system. PANTHER is another efficient protein classification database based on HMM profiles. PANTHER provides a multi-way classification of proteins on the basis of family and subfamily, molecular function, involvement in a biological process, and association with a pathway in any cellular process. It reduces the risk of redundancy by applying strict HMM scoring strategy. We also used Pfam for the classification of HPs. Pfam is a database of protein families with representative multiple sequence alignments and HMMs for each family. SVMProt was also used for functional classification of the HPs. It is a SVM based classification software trained with the dataset of about 54 functional families of protein. We performed cluster-based classification of the HPs using ProtoNet. It gives a hierarchical classification of proteins using clusters of proteins showing functional similarity. The information about the classification of the HPs is given in Supplementary Table 5."}