What is ARD2?
ARD2 is an application for the identification of alpha-rod repeats, also defined as alpha-solenoids (HEAT, Armadillo among others) in protein sequences using a neural network. Alpha-solenoids are stacks of pairs of anti-parallel helices which form together a flexible rod or wire called alpha-solenoid.
How to use ARD2?
In order to test a sequence for presence of an alpha-solenoid, one has to copy one or more sequences (sequences only or FASTA format) in the main dialogue box and hit the "Submit Query" button. A maximum of 20 sequences can be queried at the same time. Alternatively, sequences in FASTA format can be uploaded from a local file, using the "Browse" button.
What does the output of ARD2 mean?
Firstly, a general decision is displayed regarding the detected status of each sequence queried. This status could be either ALPHA-SOLENOID or NOT ALPHA-SOLENOID.
Then a more detailed output provides a score regarding the possibility that each amino-acid is at the center of an alpha-solenoid repeat. This output looks as follows:
Position, Amino acid symbol, Score, Left shift, Right shift.
- The first value indicates the position of the amino acid in the current sequence
- The second represents the amino-acid one letter code.
- The third value is the score of the neural network at the current position. It is comprised in the range [0,1[. A score equal or greater than 0.87 is associated to the presence of an alpha-solenoid repeat. The presence of a minimum of three consecutive repeats separated by a maximum of 90 residues is taken as evidence of an alpha-solenoid. A sequence comprising a minimum of three repeats in a row separated by a maximum of 90 residues constitute an alpha-solenoid.
- The last two values (Left shift and Right shift) indicate the shifts of the input windows of the neural network that gave the best score for the corresponding position. Please refer to Fournier et al. for more information.
David Fournier, Gareth A. Palidwor, Sergey Shcherbinin, Angelika Szengel, Martin H. Schaefer, Carol Perez-Iratxeta, Miguel A. Andrade-Navarro. 2013. Functional and genomic analyses of alpha-solenoid proteins. PLoS One. 8(11):e79894. Epub 2013 Nov 21. PubMed PMID:24278209.
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