About ARD

• Gareth Palidwor
• Sergey Shcherbinin
• Matthew R. Huska
• Tomas Rasko
• Ulrich Stelzl
• Anup Arumughan
• Raphaele Foulle
• Pablo Porras
• Luis Sanchez-Pulido
• Erich E. Wanker
• Miguel Andrade-Navarro.

The server

ARD is an application for the identification of alpha-rod repeats in protein sequences using a neural net. Alpha-rods are elongated structural domain composed of stacked anti-parallel alpha-helices, as described in the publication below.

Publication:

Detection of alpha-rod protein repeats using a neural network and application to huntingtin. Palidwor GA, Shcherbinin S, Huska MR, Rasko T, Stelzl U, Arumughan A, Foulle R, Porras P, Sanchez-Pulido L, Wanker EE, Andrade-Navarro MA. PLoS Comput Biol. 2009 Mar;5(3):e1000304. Epub 2009 Mar 13. PMID: 19282972

Meaning of the scores

The input window of the neural network is of 39 amino acids, which is close to the average repeat length. All residues receive scores between 0 and 1. Residues with high scores should correspond to middle residues in the hinge between the two helices of a repeat.

Reliability of scores

The parameters of the method were optimized using the analysis of proteins of known structure. We found that hits above a score of 0.8 were reliable, especially when the protein had several of them in the appropriate periodicity. Identification of a sequence as containing an alpha-rod was optimal when requiring at least three hits above a score of 0.8 with a minimum spacing of 30 amino acids between hits and a maximum of 135.

Representation and output

Scores are represented in the input sequences with a scale from red (1.0) to white (0.00). The data is also provided as a text output for input to other software.

Analysis of aligned proteins

If you have a set of aligned proteins, you can make a FASTA file of the alignment (it is one of the output options in the ClustalX multiple sequence alignment program) and use it as input of ARD. Then, use the BiasViz multiple sequence alignment viewer (http://biasviz.sourceforge.net) inputting both the FASTA file of the aligned proteins and the output file from ARD. Moreover, you can use that FASTA file for prediction of secondary structure in JPRED3 (advanced options) (http://www.compbio.dundee.ac.uk/www-jpred/); the resulting text only output can be also represented in BiasViz.

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