Riya Sethi

6 Questions 5 Answers 0 Followers

Questions related from Riya Sethi

What is the difference between sequence identity and percent identity?

Hello, I have come across a paper where it is stated that Sequence identity between these two proteins is ~36%. I performed BLAST and in the summary section, it is stated that that percent...

17 January 2024 1,443 2 View

Dock apoprotein with cofator Mg?

Hello, I am working on a protein that belongs to NUDIX family hydrolases and therefore requires Mg ion as a cofactor. But the protein that I have downloaded from PDB is an apoprotein. I want to...

12 January 2024 8,068 2 View

How to generate decoys for validation of generated pharmacophore hypothesis?

Dear all, I have developed a pharmacophore hypothesis using receptor cavity since my protein has no co-crystallized ligand. I , now, aim to validate it using a set of actives and decoys. I tried...

01 December 2023 1,384 0 View

The files generated from DUD-E are in '.picked' format. How can I use them in Schrodinger for hypothesis validation?

Also, is there a way to convert SMILES into IUPAC or common name of the compound?

01 December 2023 273 2 View

Can I dock a protein and a diadenosine polyphosphate nucleotide(protein's ligand)? If yes, then how?

I have a protein that binds to ATP and another nucleotide. I want to dock them so that I can find out the binding site residues in the protein. Which tool can I use?

11 October 2023 8,196 4 View

How can we find out the protein binding site in a protein?

I have a 3D-structure of a protein, but it is an apoprotein. I am using Maestro for molecular docking. I want to find out the protein binding site in my protein.

28 September 2023 1,720 7 View