The DynDom3D webserver for the analysis of domain movements in multimeric proteins

DynDom3D is a program for the analysis of domain movements in multimeric proteins. Its input is 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 pre-processor 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. The website can be found at: http://www.cmp.uea.ac.uk/dyndom/3D