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PEDS Advance Access originally published online on August 24, 2007
Protein Engineering Design and Selection 2007 20(10):521-523; doi:10.1093/protein/gzm042
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Short communication

The PASTA server for protein aggregation prediction

Antonio Trovato1,2, Flavio Seno1,2,3 and Silvio C.E. Tosatto4,5

1Department of Physics ‘G. Galilei’, University of Padova 2 CNISM, Padova Unit 3 INFN, Sezione di Padova 4Department of Biology and CRIBI Biotech Centre, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy

5 To whom correspondence should be addressed. E-mail: silvio.tosatto{at}unipd.it

Many different proteins aggregate into amyloid fibrils characterized by cross-ß structure. ß-strands contributed by distinct protein molecules are generally found in a parallel in-register alignment. Here, we describe the web server for a novel algorithm, prediction of amyloid structure aggregation (PASTA), to predict the most aggregation-prone portions and the corresponding ß-strand inter-molecular pairing for a given input sequence. PASTA was previously shown to yield results in excellent agreement with available experimental observations, when tested on both natively unfolded and structured proteins. The web server and downloadable source code are freely accessible from the URL: http://protein.cribi.unipd.it/pasta/.

Keywords: amyloid fibrils/cross-beta structure/parallel in-register arrangement/protein aggregation

Received May 14, 2007; revised July 4, 2007; accepted July 6, 2007.


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