Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background: The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results: In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Jiangning Song, Kevin Burrage, Zheng Yuan, Thomas Huber
• Keywords: BMCBI 2006, Multiple Sequence Alignments, Proline, Proteins