In silico platform for predicting and initiating β‐turns in a protein at desired locations. Issue 5 (25th March 2015)

• Record Type: Journal Article
• Authors: Singh, Harinder; Singh, Sandeep; Raghava, Gajendra P. S.
• Is Part Of: Proteins. Volume 83:Issue 5(2015)
• Page Start: 910
• Page End: 921
• Publication Date: 2015-03-25
• Subjects: Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.24783
• Languages: English
• ISSNs: 0887-3585

Abstract

<abstract abstract-type="main"> <title>ABSTRACT</title> <p>Numerous studies have been performed for analysis and prediction of β‐turns in a protein. This study focuses on analyzing, predicting, and designing of β‐turns to understand the preference of amino acids in β‐turn formation. We analyzed around 20, 000 PDB chains to understand the preference of residues or pair of residues at different positions in β‐turns. Based on the results, a propensity‐based method has been developed for predicting β‐turns with an accuracy of 82%. We introduced a new approach entitled "Turn level prediction method, " which predicts the complete β‐turn rather than focusing on the residues in a β‐turn. Finally, we developed BetaTPred3, a Random forest based method for predicting β‐turns by utilizing various features of four residues present in β‐turns. The BetaTPred3 achieved an accuracy of 79% with 0.51 MCC that is comparable or better than existing methods on BT426 dataset. Additionally, models were developed to predict β‐turn types with better performance than other methods available in the literature. In order to improve the quality of prediction of turns, we developed prediction models on a large and latest dataset of 6376 nonredundant protein chains. Based on this study, a web server has been developed for prediction of β‐turns and their types in proteins. This web server also predicts minimum number of mutations required to initiate or break a β‐turn in a protein at specified location of a protein. Proteins 2015; 83:910–921. © 2015 Wiley Periodicals, Inc.</p> </abstract>