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- W2912187485 abstract "In comparative modelling a protein structure can be predicted based on the structure of another protein if both proteins share sufficient sequence similarity. In the present work two potential scaling methods based on molecular dynamics (MD) simulations have been developed in order to improve structure prediction at comparative modelling of proteins and docking between proteins and small peptide ligands. The first method, presented in chapter Project 1, refers to prediction of conformation of protein loops and cyclic peptides. To accelerate the conformational sampling the rotational energy barriers of the dihedral main-chain angles and the 1-4 van der Waals and electrostatic interactions were lowered at the beginning and smoothly rescaled during the following MD simulation until the standard potential was reached. The second method, presented in chapter Project 2, was developed for modelling of side-chain conformations within protein cores and within protein-peptide interfaces. The present method uses a consecutive set of potential scaling MD simulations where the buried residues are free and the remaining protein regions are highly flexible but preserved within their overall conformation using weak positional restraints. At the beginning the non-bonded van der Waals and electrostatic interactions of selected buried side-chains were strongly alleviated and smoothly rescaled during the following steps until the total force field applied in standard MD simulations was used. In chapter Project 3 a structural model of the extracellular part of protein human Toll-like receptor 5 (TLR5) is presented, which was generated by applying comparative modelling. An X-ray structure of flagellin, the bacterial binding partner of TLR5, served subsequently for a docking approach of both components using the program ATTRACT. The docking procedure was supported by literature-based knowledge of residues located at the binding sites of both proteins." @default.
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- W2912187485 date "2005-01-01" @default.
- W2912187485 modified "2023-09-27" @default.
- W2912187485 title "Development of potential scaling methods to improve prediction of loops and binding interfaces at homology modelling and docking" @default.
- W2912187485 hasPublicationYear "2005" @default.
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