A protein structural classes prediction method based on PSI-BLAST profile

Accurate prediction of protein structural classes by incorporating PSSS and PSSM into Chou's general PseAAC

“…We select the accuracy of each class and overall accuracy as evaluation indexes which are summarized in Table 6. The compared methods include the famous methods SCPRED [17] and MODAS [19], and the other competitive methods such as RKS-PPSC [18], IEA-PSSF [72], Zhang et al [45], PSSS-PSSM [20], LCC-PSSM [73], AADP-PSSM [21] and AAC-PSSM-AC [23]. Among these methods, the PSSS-PSSM method has the best overall accuracy on the three datasets.…”

Prediction of protein structural classes for low-similarity sequences using reduced PSSM and position-based secondary structural features

“…High PSSM-scores of some proteins often indicate some possible biological evolutionary relationships between these sequences and their family (Jones, 1999;Shen and Chou, 2007;Chen et al, 2008;Liu et al, 2012;Ding et al, 2014). Here, we used PSI-BLAST program (h = 0.001 and j = 3) to search and align homogeneous sequences from SWISS-PROT database (published: May-20-2013 with 540,052 sequences).…”

“…The proposed method was first compared with AADP-PSSM , AAC-PSSM-AC (Liu et al, 2012) and Ding's method (Ding et al, 2014) based on the position specific scoring matrix. Among all the experiments, the proposed method achieved the best performance, with accuracy above 5.4-9.4% better than the next competing Ding's method (Ding et al, 2014).…”

“…Recently, Liu et al measured the average correlation between two residues separated by a g distance in a column of position specific scoring matrix and applied it to predict protein structural class (Liu et al, 2012). Ding et al extracted the long-range correlation information and linear correlation information from the PSSM (Ding et al, 2014).…”

“…Recently, several features associated with predicted secondary structures have been proposed (Chou and Cai, 2004;Altschul et al, 1997;Stormo et al, 1982;Jones, 1999;Shen and Chou, 2007;Chen et al, 2008;Liu et al, 2012;Ding et al, 2014;Kurgan and Homaeian, 2006;Kurgan et al, 2008;Zheng and Kurgan, 2008;Mizianty and Kurgan, 2009;Liu and Jia, 2010;Zhang et al, 2011;Hobohm and Sander, 1994;Zhang et al, 2013). First of all, the popular ones are widely used content of predicted secondary structural elements (content SE ), normalized count of segments (NCount), length of the longest segment (MaxSeg), normalized length of the longest segment (NMaxSeg), average length of the segment (AvgSeg), and normalized average length of the segment (NAvgSeg) .…”