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ALADYN: a web server for aligning proteins by matching their large-scale motion

2010; Oxford University Press; Volume: 38; Issue: Web Server Linguagem: Inglês

10.1093/nar/gkq293

1362-4962

Raffaello Potestio, T. Aleksiev, Francesco Pontiggia, Stefano Cozzini, Cristian Micheletti,

Microbial Metabolic Engineering and Bioproduction

The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. The latter often accompany functional conformational changes in proteins and enzymes. The ALADYN dynamics-based alignment can therefore highlight functionally-oriented correspondences that could be more elusive to sequence- or structure-based comparisons. The ALADYN server takes the structure files of the two proteins as input. The optimal relative positioning of the molecules is found by maximizing the similarity of the pattern of structural fluctuations which are calculated via an elastic network model. The resulting alignment is presented via an interactive graphical Java applet and is accompanied by a number of quantitative indicators and downloadable data files. The ALADYN web server is freely accessible at the http://aladyn.escience-lab.org address.