Data from simulations of mutations of tryptophan synthase

DOI10.5281/zenodo.10339268Zenodo10339268MaRDI QIDQ6697850FDOQ6697850

Dataset published at Zenodo repository.

Mikko Karttunen, Anupom Roy

Publication date: 10 December 2023

Copyright license: Creative Commons Attribution 4.0 International

Description

Data from the article "A Molecular Dynamics Simulation Study of the Effects of Gln114 Mutation on the DynamicBehavior of the Catalytic Site of the Tryptophan Synthase", A. Roy and M. Karttunen J. Chem. Inf. Model. (in press (2024) Web: https://doi.org/10.1021/acs.jcim.3c01966 Preprint: https://doi.org/10.26434/chemrxiv-2023-4bhpv Four systems of TS (Tryptophan Synthase): System = Denoted by E(PLP) = e-plp E(AEX1) = e-aex1 E(AA) = e-aa E(c3) = e-c3 Each system has 3 versions: wt = WildType ala114 = mutated version (Gln114 mutated to Ala114) asn114 = mutated version (Gln114 mutated to Asn114) Folder names: 1_E(PLP) System Folders 1_wt-e-plp 2_ala114-e-plp 3_asn114-e-plp 2_E(AEX1) System Folders 4_wt-e-aex1 5_ala114-e-aex1 6_asn114-e-aex1 3_E(AA) System Folders 7_wt-e-aa 8_ala114-e-aa 9_asn114-e-aa 4_E(c3) System Folders 10_wt-e-c3 11_ala114-e-c3 12_asn114-e-c3 File names: Each folder contains AMBER readable topology, restart, input files, and also last frame pdb file: initial system topology = system.parm7 initial restart file = system.rst7 minimization 1 input file = min.in minimization 1 restart file = min.rst7 minimization 2 input file = min-all.in minimization 2 restart file = min-all.rst7 heating input file = heat.in heating restart file = heat.rst7 equilibration input file = equil.in equilibration restart file = equil.rst7 production 1 input file = md.in production 1 restart file = md.rst7 production 2 input file = md2.in production 2 restart file = md2.rst7 last frame of production = frame40000_800ns.pdb

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