Optimization of the Sliding Window Size for Protein Structure Prediction

- Sliding window based methods are relatively often applied in prediction of various aspects related to protein structure. Despite their wide spread use, researchers did not establish a standard related to the size of the window, i.e., window sizes ranging between 7 and 17 residues were used in the past. To this end, this paper performs a computational study based on a probabilistic approach that aims at finding an optimal sliding window size. The results shows that formation of helical structure can be affected by amino acids (AAs) that are up to 9 positions away in the sequence, while the formation of coils and strands can be affected by AAs that are up to 3 and 6 positions away, respectively. Overall, our results suggest that a sliding window with 19 residues is optimal for secondary structure prediction, while for a specific prediction tasks, such as prediction of βstrands, a smaller window size is sufficient. Finally, the 20 AAs are categorized into five groups based on their inf...

• Type: Conference
• Year: 2006
• Where: CIBCB
• Authors: Ke Chen, Lukasz A. Kurgan, Jishou Ruan
• Keywords: CIBCB 2006, Protein Structure, Sliding Window, Window Size