Computational Bioengineering and Bioinformatics by Nenad Filipovic

Author:Nenad Filipovic
Language: eng
Format: epub
ISBN: 9783030436582
Publisher: Springer International Publishing

Further, the conformational model 10 was used as starting structure for molecular dynamics (MD) simulation. For the process of the equilibration of the system temperature of the system quickly reaches the target value (300 K), and remains stable over the remainder of the equilibration. The analysis of the interactions of the protein-ligand complex obtained after 5 ns production of MD simulation, indicates interactions with some same and also some different amino acids, comparing the complex structure obtained after molecular docking simulation. In this case, the number of hydrogen bonds between TDP1 protein and ligand are numerous, but not significant (Fig. 3). In addition, hydrogen bonds with Leu168 and Gly181 are repeated, like after the docking simulation. Also, after 5 ns of MD simulation are achieved hydrogen bonds with amino acids 147, 150, 162, 177, 178, 179, 180, 568, and those amino acids are Asp, Glu, Asn, Lys, Tyr, Asn, Ser, Ala. Amino acids Ala236 and Ala240 are included in hydrophobic alkyl and π –alkyl contacts, respectively.

Fig. 3.The stability of system during production period and formed hydrogen bonds.

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