title: FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.
abstract: We describe FRalanyzer (Fold Recognition alignment analyzer), a new web tool to visually inspect sequence-structure alignments in order to predict functionally important residues in a query sequence of unknown function. This tool is aimed at helping to infer functional relationships between a query sequence and a template structure, and is particularly useful in analyzing fold recognition (FR) results. Because similar folds do not necessarily share the same function, it is not always straightforward to infer a function from an FR result alone. Manual inspection of the FR sequence-structure alignment is often required in order to search for conservation of functionally important residues. FRalanyzer automates parts of this time-consuming process. FRalanyzer takes as input a sequence-structure alignment, automatically searches annotated databases, displays functionally significant residues and highlights the functionally important positions that are identical in the alignment. FRalanyzer can also be used with sequence-structure alignments obtained by other methods, and with structure-structure alignments obtained from structural comparison of newly determined 3D-structures of unknown function. Fralanyzer is available at http://fralanyzer.cse.buffalo.edu/.
authors.affiliation: Computer Science and Engineering Department, 201 Bell Hall University at Buffalo, Buffalo, NY 14260, USA. hksaini@cse.buffalo.edu
authors.forename: Harpreet Kaur
authors.initials: HK
authors.lastname: Saini
authors.forename: Daniel
authors.initials: D
authors.lastname: Fischer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D011506:Proteins