Using position specific scoring matrix and auto covariance to predict protein subnuclear localization

Using position specific scoring matrix and auto covariance to predict protein subnuclear localization

The knowledge of subnuclear localization in eukaryotic cells is indispensable for understanding the biological function of nucleus, genome regulation and drug discovery. In this study, a new feature representation was proposed by combining position specific scoring matrix (PSSM) and auto covariance (AC). The AC variables describe the neighboring effect between two amino acids, so that they inco...

Using support vector machine combined with auto covariance to predict protein–protein interactions from protein sequences

Compared to the available protein sequences of different organisms, the number of revealed protein-protein interactions (PPIs) is still very limited. So many computational methods have been developed to facilitate the identification of novel PPIs. However, the methods only using the information of protein sequences are more universal than those that depend on some additional information or pred...

Identifying Protein Short Linear Motifs by Position-Specific Scoring Matrix

Protein Structural Class Prediction via k-Separated Bigrams Using Position Specific Scoring Matrix

Protein structural class prediction (SCP) is as important task in identifying protein tertiary structure and protein functions. In this study, we propose a feature extraction technique to predict secondary structures. The technique utilizes bigram (of adjacent and k-separated amino acids) information derived from Position Specific Scoring Matrix (PSSM). The technique has shown promising results...

Predicting the protein disordered region using modified position specific scoring matrix

Department of Computer Science, Graduate School of Science and Engineering, Waseda University, 17 kikui-cho, Shinjuku-ku, Tokyo, 162-0044, Japan Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Aomi-Frontier 17F, 2-43 Aomi, Koto-ku, Tokyo, 135-0064, Japan 3 Pharma Design inc., Haseko Hatchobori Build, 2-19-8 Hatchobori, Chuo-ku, Tokyo, 104...