标题: How to perform the Docking DNA-Ligand for bacteria ? [打印本页] 作者Author: zako 时间: 2020-12-23 05:40 标题: How to perform the Docking DNA-Ligand for bacteria ? Hi everyone,
My problem is divided into two two parts:
I want to study the interaction DNA-ligand by Docking of some bacteria, but the problem i'm confused about which DNA sequence i should choose because according to the litterature, the bacteria has two DNA sequence (Plasmid DNA and chromsome DNA).The second problem is about the software i have to use to study this kind of Docking (DNA-Ligand), because personally i use Autodock vina, but only for Protein-ligand Docking.
Many thanks in advance. 作者Author: sobereva 时间: 2020-12-23 08:24
Personally I suggest directly running molecular dynamics for DNA-ligand system to search for optimal binding sites.作者Author: zako 时间: 2020-12-23 15:03
Dear Pr. Sobereva,
Thank you very much for your suggestion, but first i need to know which DNA i should choose.