How to do multiple docking in a single protein ?

More Pratyasha Bhowal's questions See All

What is meant by "chase cells for 24h" if no other context is provided?

"Huh7 cells were incubated for 6 h with DEN-1 sNS1 (10 ug/ml) or PBS, followed by 24 h or 48 h of chase (6 h/24 h and 6 h/48 h, respectively)." This statement is from the paper titled "The...

04 October 2023 5,082 1 View

Why is the Pymol interaction residues different from LigPlot interaction residues?

I have docked my protein with a ligand. When I am checking the polar and non polar contacts, I am getting the residues different in Pymol and LigPlot. Can someone please help me with this.

22 May 2023 9,324 4 View

I am very new to metabarcoding technique in the field of phycology. Can anyone suggest me the bioinformatics analyses for the same ?

I need to learn proper bioinformatics analysis techniques to learn ecological assessment. I am very new to learning R, and I want to know from which sites can we learn R for biological assessments.

13 July 2022 4,807 0 View

How do you calculate the log fold change of a gene with respect to control in RT-PCR?

I am using 2^(-ΔΔCt) to calculate log fold change of a gene, but some of the values are coming in decimal. For them I am using -1/(the decimal number). Please do let me know what is the rational...

04 July 2021 5,529 5 View

What is the role of cut-off wavelength in fluorescence measurement?

I am using the filter pair of 480/535 and trying to measure fluorescence. The instrument that I am using is Spectramax M2. The Cut-off filter for this pair is showing 530nm in this machine. So...

27 May 2020 861 3 View

How to quantify protein content in an enzyme having a unit of 1000 U/ml?

I am trying to quantify the protein in terms of mg/ml by BCA assay with an activity of 1000 u/ml.

23 December 2019 4,462 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

What are the steps of formulating a herbal extract into a sheep/goat drench?

I am working on natural remedies for de-worming in small ruminant livestocks. Part of my project involves formulation of drench-type product, which I have not much experience in. My experience is...

30 July 2024 9,806 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

Has the Affordable Connectivity Program Helped You/Your Community? And Would Bulk Tablets on a Similar Program Help Your Business?

Do You Believe VP Harris Would Show Empathy to Tech Companies in Her Administration as POTUS? I ask in light of the fact that, the ACP was not re-funded this round. So many and businesses need...

24 July 2024 4,732 3 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 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

How to calculate theoretical Ki from the docking results?

I have used Schrödinger (Glide) for docking

13 July 2024 3,003 1 View

Is the protecting group boc of the amino group stable at 37°C?

I have a small molecule reagent with a boc-protected amino group. Now the reaction needs to be reacted at 37°C for 30 h. Is this protection group stable?

12 July 2024 3,745 2 View

Jobin Thomas

You can use Autodock Vina.

Mohamed asif Shajahan

I agree with Mr. Jobin Thomas , but putting it into practise would be the most challenging aspect.

so you can try EasyDockVina2 for multiple ligand docking

Code EasyDockVina2: Graphical User Interface for Ligand Optimizat...

Amanpreet Kaur

You can use autodock vina or pyrx for multiple docking

Pratyasha Bhowal

Thank you so much. I have been able to do it.