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001034039 037__ $$aFZJ-2024-06869
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001034039 1001_ $$0P:(DE-Juel1)184777$$ade Bruyn, Emile$$b0$$eFirst author
001034039 245__ $$aMolecular Dynamics Trajectories Exploring the Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution
001034039 260__ $$aJülich$$bForschungszentrum Jülich$$c2024
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001034039 520__ $$aPrimary data for the publication 'Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution' by de Bruyn, Dorn, Rossetti, Fernandez, Outeiro, Schulz and Carloni. Submitted to the Journal of Chemical Information and Modeling. Included are all GROMACS input files, parameterised topologies, starting and final configurations, and trajectories for the lowest temperature replica (at 300 K, lowest of 32 replicas between 300-500 K exchanging according to the REST2 algorithm (Wang et al. 2011)). The data is split into three archives: all_atom_trajectories.zip contains all input files and all atom trajectories including solvent trajectories written at 100 ps intervals protein+ion_trajectories.zip contains configuration/non-parameterised topologies and trajectories excluding solvent, but including ions trajectories written at 10 ps intervals additional_simulations.zip contains the all atom trajectories and input files, and solvent-free trajectories above, for the additional simulations in the Supplemental Information of the article: includes the DES-Amber-based simulations with 64 replicas between 300-600 K, and a99SB-disp-based simulations   Folders are named according to the following top level scheme: DES-Amber simulations/ Simulations created using the DES-Amber force field (Tucker et al. 2022) a99SB-disp simulations/ SImulations created using the a99SB-disp force field for Intrinsically Disordered Proteins (IDPs) (Robustelli et al. 2018) Sub-folders follow the following scheme: AS/ Simulations of the physiological form of wild-type Human α-Synuclein unphosphorylated pAS/ Simulations of the physiological form of wild-type Human α-Synuclein phosphorylated at S129 with double negative charge pASH/ Simulations of the physiological form of wild-type Human α-Synuclein (a99SB-disp simulations only) phosphorylated at S129 with a single negative charge (monoprotonated)
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001034039 650_7 $$2Other$$aStructural biology
001034039 650_7 $$2Other$$aBiophysics
001034039 650_7 $$2Other$$aPTM
001034039 650_7 $$2Other$$aPhosphorylated Proteins
001034039 650_7 $$2Other$$aPhosphorylation
001034039 650_7 $$2Other$$aaSyn
001034039 650_7 $$2Other$$aAS
001034039 650_7 $$2Other$$aAlpha-Synuclein
001034039 650_7 $$2Other$$aMolecular Dynamics
001034039 7001_ $$0P:(DE-Juel1)201609$$aDorn, Anton$$b1$$eFirst author$$ufzj
001034039 7001_ $$0P:(DE-Juel1)145921$$aRossetti, Giulia$$b2$$eCorresponding author
001034039 7001_ $$00000-0003-0454-7735$$aFernandez, Claudio Oscar$$b3
001034039 7001_ $$00000-0003-1679-1727$$aOuteiro, Tiago Fleming$$b4
001034039 7001_ $$0P:(DE-Juel1)171786$$aSchulz, Jörg B.$$b5
001034039 7001_ $$0P:(DE-Juel1)145614$$aCarloni, Paolo$$b6$$eLast author
001034039 773__ $$a10.5281/zenodo.12605635
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