Hello fellow researchers,
I am currently working on molecular docking using CB-Dock2, and I encountered an issue where I received a message stating "The chains of the uploaded protein are broken." As a result, the docking process was not completed. I would greatly appreciate your insights and suggestions on how to improve the structure of the protein to overcome this problem.
Thank you in advance for your valuable input!
Best regards,
Tahmineh
Have you checked the protein structure and have you energy minimized it???
Is there any particular reason for using CB DOCK2 for initiating the docking protocol???
You can use AutoDockTools for the same which is an open source software.
Regards
Jobin Thomas Thank you for your response! No resean for using this software. I am working on a project based on prevoius literature. I could check the protein structure and found its chain was brocken. Now I could solve my problem by using Chemira. But I am trying to test other softwares too.
I give you some tips about performing molecular docking. First, you need to make sure that your protein structure is complete and has no missing atoms or residues.
Second, you can optimize the geometry and energy of your protein structure before docking. You can use tools like GROMACS to perform molecular dynamics simulations and energy minimization on your protein structure.
Third, you need to prepare your protein structure for docking by adding hydrogen atoms, assigning charges, and defining flexible regions. You can use tools like AutoDockTools or PyMOL to do these tasks.
Finally, you need to select a suitable docking algorithm and scoring function for your docking problem. CB-Dock2 may not be the best choice for your protein. You can try other docking tools like AutoDock Vina that use different algorithms and scoring functions.
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