How to select active site residues for site-specific docking?

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How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

How to prepare the nanoparticle treated fungal sample for Environmental SEM analysis?

A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.

07 August 2024 5,307 1 View

Is VSM measurment of NdFeB alloy powder sample require any spesific sample preparation ?

Is any specific sample preparation required to perform VSM measurement of NdFeB alloy powder to get a square-shaped M-H loop? Or is it mandatory to make magnetically aligned and sintered pellets...

09 July 2024 1,969 0 View

How to see whether my protein is aggregated using western blotting?

I am working on one protein which gets aggregated (similar to alpha-synuclein and tau) in certain neurodegenerative diseases. I am trying to confirm the aggregation using Western blotting....

30 June 2024 5,060 3 View

How can i calculate the band alignmet of Sc2CO2/BlueP heterostructure from DFT?

I know the work function and band gap of each monolayer and heterostructure. I calculated mulliken electronegativity(X) of Sc2CO2 and Bluep. From that i found Ev = X- 4.5+Eg Ec = Ev-Eg, where Eg...

28 June 2024 9,360 0 View

How to get Consistency Ratio when scale of relative importance is used in AHP?

In AHP (Analytical Hierarchical Process) using 9 criteria, when I use a a scale of relative importance (1-9), I am getting a higher lambda-max and hence an inconsistent Consistency Ratio (>.10)...

16 June 2024 1,228 1 View

Can we use any inferential statistics on a data set measured using non-validated questionnaires?

I have heard from my senior scholars that we can't use a non-validated scale to measure variables in a correlational study. Is it true? Can anyone help me with finding a reference for the same.

05 June 2024 7,851 4 View

How to get 2 Octanol from Castor oil at a laboratory scale ?

Any latest method developed

24 May 2024 2,128 1 View

What are recent UWB Antennas ?

I require recent UWB antennas manufactured

15 May 2024 3,888 1 View

How to export Chlorophyll Concentration output from SNAP Software?

Dear All, We have downloaded sentinel 2 data for measuring Chlorophyll Concentration in seawater. We have processed sentinel 2 data in SNAP software and also applied standard...

15 May 2024 3,339 1 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 3 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 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 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

Can we analyse RMSD for peptide-HLA docking and binding affinity for peptide-HLA to TCR docking, in a peptide-HLA-TCR docking ?

In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?

11 July 2024 4,831 0 View

Looking for a bioinformatics expert especially one who has expertise in Nanoparticles docking ?

Silver Nanoparticles docking with alpha amylase and alpha glusidase .

11 July 2024 6,883 2 View

Mario E. Valdés-Tresanco

Deepasree K. check this tutorial

https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki/4.2.4-Automatic-mode-using-AutoDock-Vina

Waseem Ahmad Ansari

Deepasree K. Hi

Hope you will be ok

You can use prosite and CASTp servers for identifying active site, these are reported servers and sites in your articles.

Deepasree K.

Thank you for the information. Mario E. Valdés-Tresanco , Waseem Ahmad Ansari and Maysaa Alakbaree