Article
Dynamics alignment: Comparison of protein dynamics in the scop database
Dror Tobi,
Corresponding Author
Dror Tobi
Department of Computer Sciences and Mathematics, Ariel University Center of Samaria, Ariel 40700, Israel
Department of Molecular Biology, Ariel University Center of Samaria, Ariel 40700, Israel
Department of Computer Sciences and Mathematics, Ariel University Center of Samaria, Ariel 40700, Israel===Search for more papers by this authorDror Tobi,
Corresponding Author
Dror Tobi
Department of Computer Sciences and Mathematics, Ariel University Center of Samaria, Ariel 40700, Israel
Department of Molecular Biology, Ariel University Center of Samaria, Ariel 40700, Israel
Department of Computer Sciences and Mathematics, Ariel University Center of Samaria, Ariel 40700, Israel===Search for more papers by this authorAbstract
A novel methodology for comparison of protein dynamics is presented. Protein dynamics is calculated using the Gaussian network model and the modes of motion are globally aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. The alignment is fast and can be used to analyze large sets of proteins. The methodology is applied to the four major classes of the SCOP database: “all alpha proteins,” “all beta proteins,” “alpha and beta proteins,” and “alpha/beta proteins”. We show that different domains may have similar global dynamics. In addition, we report that the dynamics of “all alpha proteins” domains are less specific to structural variations within a given fold or superfamily compared with the other classes. We report that domain pairs with the most similar and the least similar global dynamics tend to be of similar length. The significance of the methodology is that it suggests a new and efficient way of mapping between the global structural features of protein families/subfamilies and their encoded dynamics. Proteins 2012; © 2011 Wiley Periodicals, Inc.
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