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J Comput Biol. 2016 Jan;23(1):21-6. doi: 10.1089/cmb.2015.0143. Epub 2015 Nov 5.

The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins.

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D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia , Norwich, United Kingdom .


DynDom3D is a program for the analysis of domain movements in multimeric proteins. Its inputs are two structure files that indicate a possible domain movement, but the onus has been on the user to process the files so that there is the necessary one-to-one equivalence between atoms in the two atom lists. This is often a prohibitive task to carry out manually, which has limited the application of DynDom3D. Here we report on a webserver with a preprocessor that automatically creates an equivalence between atoms using sequence alignment methods. The processed structure files are passed to DynDom3D and the results are presented on a webpage that includes molecular graphics for easy visualization.


protein structure; sequence analysis; structural and functional genomics

[Indexed for MEDLINE]

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