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Gewählte Doctoral Thesis:

Christian Margreitter (2016): From amino acids to proteins: on the parametrization and automation of molecular simulation.
Doctoral Thesis - Institut für Molekulare Modellierung und Simulation (MMS), BOKU-Universität für Bodenkultur, pp 268. UB BOKU obvsg FullText

Data Source: ZID Abstracts
Abstract:
Molecular dynamics simulations have evolved into a broadly used and reliable tool in recent decades. The key to this progress are both increasingly powerful computers and the higher accuracy of our computational models, which are constantly improved. This thesis' first goal is to support the latter developments by working on a better description of phosphate moieties and the amino acid backbone torsions in the context of GROMOS parameter sets. Phosphates are pivotal in the nucleic acids' backbone, lipids and as a major group of protein post-translational modifications. The backbone torsions on the other hand are utilized in every simulation using peptides and proteins and therefore of high importance. The second aim was to link simulations and experiments of antibodies by the establishment of an in-silico binding prediction approach. Experimentally verified, it allows to get a qualitative forecast on the antibodies' binding behaviour from simulations without the hassle to calculate full binding free energies. This type of large projects made an automated workflow, simulating multiple candidates automatically, highly advantageous. We have therefore implemented the molecular dynamics workflow manager PROMETHEUS. It allows to define a workflow logic for a distinct project and to subsequently perform the execution completely automated an arbitrary number of times for all subjobs part of the project. Furthermore, in order to readily see the results afterwards and to provide the user with publishable figures, the R package MDplot has been developed, which is able to parse and plot the simulation data directly. This work tries to push the boundaries of molecular dynamics simulations in terms of accuracy and applicability further, by provision of appropriate computational tools and force field parameters.

Betreuer: Oostenbrink Chris
1. Berater: Schöll-Paschinger Elisabeth

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