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Nucleic Acids Res. 2011 Jul;39(Web Server issue):W357-61. doi: 10.1093/nar/gkr468. Epub 2011 Jun 14.

MarkUs: a server to navigate sequence-structure-function space.

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Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.


We describe MarkUs, a web server for analysis and comparison of the structural and functional properties of proteins. In contrast to a 'structure in/function out' approach to protein function annotation, the server is designed to be highly interactive and to allow flexibility in the examination of possible functions, suggested either automatically by various similarity measures or specified by a user directly. This is combined with tools that allow a user to assess independently whether or not a suggested function is consistent with the bioinformatic and biophysical properties of a given query structure, further allowing the user to generate testable hypotheses. The server is available at

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