Hauptseite > Publikationsdatenbank > SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories > print

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024 7 _ |a 10.3390/biology12040581
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100 1 _ |a de Bruyn, Emile
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245 _ _ |a SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories
260 _ _ |a Basel
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520 _ _ |a The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion–residue interactions play an important role in the structures and behaviors of IDPs.
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536 _ _ |a HDS LEE - Helmholtz School for Data Science in Life, Earth and Energy (HDS LEE) (HDS-LEE-20190612)
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700 1 _ |a Dorn, Anton
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700 1 _ |a Zimmermann, Olav
|0 P:(DE-Juel1)132307
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700 1 _ |a Rossetti, Giulia
|0 P:(DE-Juel1)145921
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770 _ _ |a Intrinsically Disordered Proteins Interactions with Their Molecular Environment at the Crossroad between Theory and Experiments
773 _ _ |a 10.3390/biology12040581
|g Vol. 12, no. 4, p. 581 -
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|t Biology
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856 4 _ |u https://juser.fz-juelich.de/record/1006780/files/biology-12-00581-v2.pdf
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