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XSuLT: a web server for structural annotation and representation of sequence-structure alignments

Published version
Peer-reviewed

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Type

Article

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Authors

Ochoa-Montaño, B 
Blundell, TL 

Abstract

The web server XSuLT, an enhanced version of the protein alignment annotation program JoY, formats a submitted multiple-sequence alignment using three-dimensional (3D) structural information in order to assist in the comparative analysis of protein evolution and in the optimization of alignments for comparative modelling and construct design. In addition to the features analysed by JoY, which include secondary structure, solvent accessibility and sidechain hydrogen bonds, XSuLT annotates each amino acid residue with residue depth, chain and ligand interactions, inter-residue contacts, sequence entropy, root mean square deviation and secondary structure and disorder prediction. It is also now integrated with built-in 3D visualization which interacts with the formatted alignment to facilitate inspection and understanding. Results can be downloaded as stand-alone HTML for the formatted alignment and as XML with the underlying annotation data. XSuLT is freely available at http://structure.bioc.cam.ac.uk/xsult/.

Description

Keywords

amino acids, entropy, happiness, hydrogen, ligands, protein structure, secondary, solvents, inspection, xml

Journal Title

Nucleic Acids Research

Conference Name

Journal ISSN

0305-1048
1362-4962

Volume Title

45

Publisher

Oxford University Press
Sponsorship
Medical Research Council (MR/M026302/1)
Medical Research Council (MR/N501864/1)
Wellcome Trust (093167/Z/10/Z)
Wellcome Trust (200814/Z/16/Z)
Bill & Melinda Gates Foundation [RG60453 to B.O.M.]; Bill & Melinda Gates HIT-TB (to T.L.B.); EU MM4TB [260872 to T.L.B.]; Wellcome Trust Programme Grant [093167/Z/10/Z to T.L.B.] and Investigator Award [200814/Z/16/Z to T.L.B.]; Medical Research Council Newton Fund RCUK-CONFAP Grant [MR/M026302/1 to T.L.B.]. Funding for open access charge: Wellcome Trust.