title: The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins.
abstract: 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.
authors.affiliation: D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia , Norwich, United Kingdom .
authors.forename: Christopher
authors.initials: C
authors.lastname: Girdlestone
authors.affiliation: D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia , Norwich, United Kingdom .
authors.forename: Steven
authors.initials: S
authors.lastname: Hayward
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001221:Aspartate Carbamoyltransferase / Q000737:chemistry; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software
chemical_list: D011506:Proteins; D001221:Aspartate Carbamoyltransferase
keywords: protein structure; sequence analysis; structural and functional genomics