title: ALADYN: a web server for aligning proteins by matching their large-scale motion.
abstract: 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.
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati and eLab, via Bonomea 265, 34136 Trieste, Italy.
authors.forename: R
authors.initials: R
authors.lastname: Potestio
authors.forename: T
authors.initials: T
authors.lastname: Aleksiev
authors.forename: F
authors.initials: F
authors.lastname: Pontiggia
authors.forename: S
authors.initials: S
authors.lastname: Cozzini
authors.forename: C
authors.initials: C
authors.lastname: Micheletti
mesh_terms: D053829:Amyloid Precursor Protein Secretases / Q000737:chemistry; D003546:Cysteine Endopeptidases / Q000737:chemistry; D005090:Exodeoxyribonucleases / Q000737:chemistry; D016333:HIV Protease / Q000737:chemistry; D020407:Internet; D009038:Motion; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins; D005090:Exodeoxyribonucleases; C020133:exodeoxyribonuclease III; D053829:Amyloid Precursor Protein Secretases; D003546:Cysteine Endopeptidases; C091827:adenain; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1
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