Protein contact order prediction from primary sequences

Background: Contact order is a topological descriptor that has been shown to be correlated with several interesting protein properties such as protein folding rates and protein transition state placements. Contact order has also been used to select for viable protein folds from ab initio protein structure prediction programs. For proteins of known three-dimensional structure, their contact order can be calculated directly. However, for proteins with unknown three-dimensional structure, there is no effective prediction method currently available. Results: In this paper, we propose several simple yet very effective methods to predict contact order from the amino acid sequence only. One set of methods is based on a weighted linear combination of predicted secondary structure content and amino acid composition. Depending on the number of components used in these equations it is possible to achieve a correlation coefficient of 0.857

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Yi Shi, Jianjun Zhou, David Arndt, David S. Wishart, Guohui Lin
• Keywords: BMCBI 2008, Contact Order, Protein, Three-dimensional Structure