TY - JOUR
T1 - FRalanyzer
T2 - A tool for functional analysis of fold-recognition sequence-structure alignments
AU - Saini, Harpreet Kaur
AU - Fischer, Daniel
N1 - Funding Information:
The Fischer lab is supported by grants from the NIH and Genefun. We thank the developers of PDBSum and Roman Laskowski for his support. Funding to pay the Open Access publication charges for this article was provided by a grant from the NIH.
PY - 2007/7/1
Y1 - 2007/7/1
N2 - 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 sequencestructure 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/.
AB - 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 sequencestructure 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/.
UR - http://www.scopus.com/inward/record.url?scp=34547597225&partnerID=8YFLogxK
U2 - 10.1093/nar/gkm367
DO - 10.1093/nar/gkm367
M3 - Article
AN - SCOPUS:34547597225
SN - 0305-1048
VL - 35
SP - W499-W502
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - SUPPL.2
ER -