PMC:4331676 / 34080-34990 JSONTXT

{"project":"2_test","denotations":[{"id":"25708928-24475169-14842666","span":{"begin":209,"end":211},"obj":"24475169"},{"id":"25708928-19385697-14842667","span":{"begin":830,"end":832},"obj":"19385697"},{"id":"25708928-16551468-14842668","span":{"begin":860,"end":862},"obj":"16551468"},{"id":"25708928-19911048-14842669","span":{"begin":883,"end":885},"obj":"19911048"}],"text":"In order to further compare the predictive performance of SVM-PSSM-DT with other existing methods, we evaluated the proposed method on the independent dataset PDB186. It was recently constructed by Lou et al [75] to validate the quality of predictions, which consists 93 DNA-binding proteins and equal number of non DNA-binding proteins selected from PDB. Since there are some sequences from the benchmark dataset that shared high sequence identity with the independent dataset PDB186, the tool CD-HIT [77] was applied to remove the sequences from the benchmark dataset having more than 25% sequence identity to any one in a same subset in the independent dataset PDB186 to avoid homology bias. Table 4 lists the predictive results of the proposed method and several relevant existing methods, including iDNA-Prot [16], DNA-Prot [74], DNAbinder [21], DNABIND [34], and DNA-Threader [78], to our best knowledge."}