In many cellular signaling pathways in cancer cells, the expression of many genes rises. One result of this excessive expression is cellular traffic and unwanted interactions between proteins. Therefore, it is important to examine the interactions and identify the amino acids involved in the interactions. There are several ways to examine the interactions such as string and using molecular docking. Today, many Docking softwares are active on web servers like Haddock, cluspro, zdock, etc; but, to my mind, examining the interaction between proteins using docking, based on several different reasons, has low credibility that makes the results of these softwares unreliable. That's why I decided to examine it with a better method. For this purpose, I used the molecular dynamics simulation method to locate the molecules under dynamic conditions to make it easier to study the interactions between amino acids (fluctuations, pi pi, hydrogen, and electrostatic bonds). The procedure is as follows: 1- Two proteins were received from the RCSB site. 2- Two proteins were placed at 6-angstrom distance using the Discover Studio software. First question is: Please suggest another way to do this procedure via software (considering the desired position) (according to the available data in the literature) (i.e. the hot spot amino acids) (involved in the interaction) to place two proteins of appropriate position in front of each other? And the next question is whether the 6-angstrom gap between two proteins is sufficient? 3- From the topology building process with pdb2gmx to indexing like the rest of the Justin Lamquell site tutorials were done (Multiple chain tutorial). But the problem is choosing the size of the box to reduce the simulation time. Please suggest a way to find the appropriate box size for two proteins in a box. 4- In order to force the interaction of two proteins, the Pull code tutorial was used. It should be noted that a protein was used to capture RMSD; i.e. the protein stabilization was screened. Please suggest a more precise way to analyze, develop, and validate this method. -- Gromacs Users mailing list
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