title: MarkUs: a server to navigate sequence-structure-function space.
abstract: 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 http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Mark-Us.
authors.affiliation: Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
authors.forename: Markus
authors.initials: M
authors.lastname: Fischer
authors.forename: Qiangfeng Cliff
authors.initials: QC
authors.lastname: Zhang
authors.forename: Fabian
authors.initials: F
authors.lastname: Dey
authors.forename: Brian Y
authors.initials: BY
authors.lastname: Chen
authors.forename: Barry
authors.initials: B
authors.lastname: Honig
authors.forename: Donald
authors.initials: D
authors.lastname: Petrey
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D020407:Internet; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000502:physiology; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D001426:Bacterial Proteins; D011506:Proteins