Chong Qi

6 Questions 11 Answers 0 Followers

Questions related from Chong Qi

How to generate 2D interaction map for docking with a multichain peptide?

I have performed molecular docking with autodock vina for insulin (consists of chain A and B) and a DNA aptamer. I could not analyze the data using pymol following online tutorial, as no...

09 June 2025 8,939 5 View

Is there any way to directly predict 3D structure of a ssDNA sequence rather than going through the step-by-step conversion from DNA-RNA-DNA?

I would like to predict the 3D structure of ssDNA aptamer sequence but I cant find any tool for DNA 3D structure prediction, but only available for RNA. Several articles mentioned to convert the...

23 April 2025 8,019 2 View

Docking exceeded maximum torsion, how should I decided which to remove?

Im running molecular docking on insulin and a DNA sequence, but the insulin is having to many torsions (140 active torsion but the maximum torsion allowed is only 32 with autodock vina)....

04 April 2025 5,988 6 View

Different docking results were obtained when the grid box center changes a little bit, but both covering the whole receptor. Why?

I was doing blink docking using AutoDock Vina. All the parameters are same, ligand and receptor also the same, just that the grid box center is a little bit different (I did at different time...

16 December 2024 9,714 2 View

Trying to dock insulin-receptor but was failed, stated to try again with smaller molecule. Is it because the target(ins) too big? How should I do?

Hi guys, I am trying to design an aptamer for insulin via in silico methods. I used aptcad webserver for docking but kept showing failed, stated to try again with smaller molecule. Is it because...

06 November 2024 2,553 3 View

How to select proper PDB structure? Prior to molecular docking, how to identify and fix errors with the pdb structure?

I am having problem in the selection of monomeric human insulin pdb structure for the development of aptamer via molecular docking and molecular dynamics. How should I select the best suit one...

01 January 1970 8,822 5 View