John Michael Stewart

5 Questions 13 Answers 0 Followers

Questions related from John Michael Stewart

To what extent (if any) do different small molecule docking programs take into account halogen bonding and pi-pi stacking interactions?

I am working with small molecules that seem likely to facilitate pi-pi stacking interactions and/or halogen bonding. I am curious to know whether any small molecule docking/screening freeware...

25 November 2014 3,660 10 View

What is the best structure-based method for finding compounds with similar structures to other specific small molecules?

I have two small molecules with similar structures. I want to determine if there are other compounds which display structural similarities. I know it may be possible to make a pharmacophore to do...

17 January 2014 4,854 6 View

Is it possible to exclude interactions with particular side chains during docking with autodock vina?

I want to restrict which residues my small molecules will interact with. Several of the near by residues can be variable. However I can not restrict the search grid to this area because the...

12 October 2013 9,388 7 View

Is it possible to use Ubuntu with a boot disk or flash drive to run molecular dynamics/modeling software on a machine that normally runs windows?

Most people know that Linux has the most software support for molecular modeling and molecular dynamics. I would like to be able to run Ubuntu Linux for this purpose on my Windows machine. I am...

08 October 2013 5,237 3 View

What is a reasonable molar ratio of small molecule to protein when screening compounds for their ability to inhibit protein-protein interactions?

I have 10 mg each of ~30 small molecules I want to screen for their ability to rescue cofactor activity after addition of a protein cofactor inhibitor. These compounds are the first that will be...

27 May 2013 1,373 10 View