During docking of multiple ligands with glide in XP after ligand docking only one ligand present in in glide-dock_XP_1_pv.maegz file, what is problem?

More Somdatta Yashwant Chaudhari's questions See All

Which has major role in nutrition, Prebiotics or probiotics?

It Seems that the major role is on pre-biotics and its supplement. But as far as the gut health is concerned there is major role of Pro-biotics also. So, i would like to know the expert opinions...

30 January 2024 6,682 4 View

Box-Behnken design in Response Surface Design got result ?

why Lack of Fit P-values show star *

01 January 2024 330 3 View

What is the importance of Dilation Angle in ABAQUS simulation software?

I am working on ABAQUS to simulate the behavior of a reinforced concrete deep beam. I am facing the issue of the Dilation Angle in that. Can anyone please guide me to solve this issue?

03 May 2023 8,009 0 View

How to get y+ value in Ansys CFX ?

I am working on simulation of savonius hydrokinetic turbine in cfx. I have set inflation layer on turbine as shown in photos. It is observed in the previous investigation that, the non-dimensional...

23 April 2023 2,983 3 View

Does letter to editor has same weightage as of Publication?

As there is section, Letter to Editor, does it carries equal weightage as the regular research paper.

03 April 2023 6,580 1 View

How to do methanolic extract of plant oil?

I am taking half quantity of oil and half quantity of methanol, than vertex for 10 min to mix it. Than the upper methanolic portion collecting in other tube or vessel and keeping for methanol...

19 March 2023 5,413 0 View

What are the C4 plants and how they are useful in Tropical Countries?

I want to know about the C4 pathway of Plants and the usefulness of C4 plants in the present scenario where consistent Geo-climatic changes are occurring and role of C4 plants in assuring food...

05 March 2023 399 0 View

Does increasing primer concentration in qPCR increase or decrease the PCR efficiency?

I am trying to develop a standard curve for miRNA using qPCR. I keep getting Ct vs log(mass) slopes around -5, which is much lower than -3.3 (100% PCR efficiency). I am looking for advice on how...

22 February 2023 4,041 3 View

What is the exact difference between Shelf Life and Expiry Date?

Does the Shelf Life is different from Expiry for Drugs as well as Food? If it is different then what is the exact difference?

01 February 2023 6,901 1 View

Is 'Pharmaceutics and Pharmacology Research' a predatory journal?

It continuously mailing for paper etc.

08 January 2023 6,584 2 View

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

Is it possible to dock more than one drug in the same active site or pocket of a protein to study synergistic/antagonistic/additive properties?

I wanted to know whether we can observe the synergistic/antagonistic/additive properties of combinations or mixtures of compounds through docking analysis. But during docking preparation any...

28 July 2024 7,413 6 View

What is the main factor involve in higher binding score performing molecular docking?

A molecule shows the -11.6 kcal/mol and second one -8.0 kcal/mol so why molecule (A) revealed higher binding score. Please explain major factor involve in it.

21 July 2024 954 5 View

In silico can we join two ligands for docking....?

I have performed docking of proteins with two ligands, both ligands show affinity. I want to check the effect if we join both ligands and perform docking

20 July 2024 2,653 2 View

How to determine LOD values?

I am performing fluorescence experiments using a ligand to detect metal ions. I want to determine the Lowest Detection Limit (LOD) using the formula LOD = 3σ / K. However, I'm uncertain about...

19 July 2024 1,086 1 View

How to extract binding energy from pv.maegz file without using Schrodinger?

I have conducted virtual screening using Schrödinger on a database of 17,000 molecules. Unfortunately, I cannot use the system with the Schrödinger license at the moment. I am trying to find a way...

18 July 2024 2,881 4 View

Mohamed AbdElAziz Khamis Omar

Article Flexible Ligand Docking with Glide

https://www.schrodinger.com/kb/669

https://www.researchgate.net/post/How_can_I_dock_multiple_ligands_to_each_pocket_of_each_monomer_of_a_homotetrameric_protein

https://www.researchgate.net/post/Is_it_possible_to_dock_multiple_ligands_with_a_single_protein_in_AutoDock_42

http://bio3d.uib.no/pdfs/docking.pdf

Mokhtar Nosrati

Hi, I think this reflect ligand- target affinity, maybe only one compound has effective interaction against your target