Dataset Information

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/.

SUBMITTER: Saini HK

PROVIDER: S-EPMC1933221 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature

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FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.

Saini Harpreet Kaur HK Fischer Daniel D

Nucleic acids research 20070530 Web Server issue

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 straightfor ...[more]

PMID: 17537819

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Project description:BackgroundSeveral methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by different methods.ResultsWe analysed and compared the structural alignments obtained by different methods using three sets of pairs of structurally related proteins. The first set corresponds to 355 pairs of remote homologous proteins according to the SCOP database (ASTRAL40 set). The second set was derived from the SISYPHUS database and includes 69 protein pairs (SISY set). The third set consists of 40 pairs that are challenging to align (RIPC set). The alignment of pairs of this set requires indels of considerable number and size and some of the proteins are related by circular permutations, show extensive conformational variability or include repetitions. Two standard methods (CE and DALI) were applied to align the proteins in the ASTRAL40 set. The extent of structural similarity identified by both methods is highly correlated and the alignments from the two methods agree on average in more than half of the aligned positions. CE, DALI, as well as four additional methods (FATCAT, MATRAS, Calpha-match and SHEBA) were then compared using the SISY and RIPC sets. The accuracy of the alignments was assessed by comparison to reference alignments. The alignments generated by the different methods on average match more than half of the reference alignments in the SISY set. The alignments obtained in the more challenging RIPC set tend to differ considerably and match reference alignments less successfully than the SISY set alignments.ConclusionThe alignments produced by different methods tend to agree to a considerable extent, but the agreement is lower for the more challenging pairs. The results for the comparison to reference alignments are encouraging, but also indicate that there is still room for improvement.

Dataset Information

FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.

Publications

FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.

Similar Datasets

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