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

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/.

MSALigMap—A Tool for Mapping Active-Site Amino Acids in PDB Structures onto Known and Novel Unannotated Homologous Sequences with Similar Function

“…The ligand binding sites mapped using one or many crystal structures can be applied to several sequences and be reliable, as long as the protein sequences have similar function and sequence similarity greater than 30%, a typical cut off for protein modelling. Other very useful similar tools exist online, but they have limitations related to showing the binding sites of the sequence (e.g., XSult [20] or Alignment-Annotator web server [36]) or they have limited annotations (e.g.,…”

“…The ligand binding sites mapped using one or many crystal structures can be applied to several sequences and be reliable, as long as the protein sequences have similar function and sequence similarity greater than 30%, a typical cut off for protein modelling. Other very useful similar tools exist online, but they have limitations related to showing the binding sites of the sequence (e.g., XSult [20] or Alignment-Annotator web server [36]) or they have limited annotations (e.g., the SwissRegulon database of genome-wide annotations of regulatory sites currently has only 17 prokaryotes and 3 eukaryotes in their collection [37,38]. Thus, the proposed MSALigMap tool is novel and not limited in capabilities in terms of showing the binding sites in the sequence output for protein-ligand, protein-peptide, and protein-DNA complexes.…”

“…Many structure-based tools, such as LigAlign [18] and GASS-WEB [19], are available for mapping binding pockets using protein structures. Recently, it was reported that XSuLT, a web-based server, can be used for sequence annotation using structural information [20]. However, this tool cannot be used for mapping the DNA binding sites of transcription factor proteins.…”