Zhe Li

5 Questions 7 Answers 0 Followers

Questions related from Zhe Li

Is there a force field with reliable parameters for 5' phosphate of DNA?

Hello! I trying to do some molecular dynamics with DNA structures, where I am checking how 5' phosphate affects the interaction. However, in common force field such as AMBER, no charge set was...

19 November 2018 3,896 4 View

What is the most affordable DNA-protein complex for crystallization?

Hi! Just want to know whether there are some very common DNA-protein complex for crystallization? Whatever proteins are fine. But I prefer cheaper and well-studied ones for crystallography...

12 December 2016 4,402 2 View

Why Electrophoretic Mobility Shift Assays (EMSA) is always measured at DNA concentration below Kd?

Hi! I am doing some EMSA and got some questions on the basics (not much experience in biochem), could anyone give me some help? Many thanks! So why do we usually use low DNA concentration in this...

17 November 2016 7,563 2 View

How to build protein interface model basing on existing pdb file?

Hi guys, Does anyone know something about building pdb models in this special case? So now I have a pdb file with DNA and protein binding (1 to 1) together. So how could I build another model with...

28 April 2016 5,528 2 View

What are general characterization methods for DNA-binding protein?

Hi friends, Recently working on some DNA-binding proteins. The dissociation constant is in nanomolar range. Anyone having experience with these DNA binding proteins knows any easy way to...

07 January 2016 4,807 7 View