Multiple ligands-receptors docking

More Ergin Karatekin's questions See All

How can we calculate the elasticity or marginal effect of parameters in latent class model?

How can we calculate the elasticity or marginal effect of parameters in a latent class model? The latent class model is created with covariates, and the dependent and independent variables are...

14 January 2024 6,235 0 View

PCR Sample Purification, what is the difference between KOH and NaOH?

I have 2 protocols for PCR sample purification. One uses Sodium for salt and other is using Potassium for salt. What is the reason for using different chemicals for salt in purification protocols....

06 September 2023 9,128 3 View

Can a gene be cloned along with the intron?

Hello, dear researchers. I am interested in a gene in Pombe. The gene contains 2 introns. I want to overexpress this gene in Pombe. Can I amplify and clone the gene by PCR or do I need to do cDNA...

04 September 2023 4,525 4 View

After purification from agarose gel, DNA concentration cannot be measured in the nanodrop, but can be visualized in the gel. What could be the reason?

Hello dear researchers. After gel purification of the plasmid cut with restriction endonucleases, I cannot take measurements on a nanodrop. However, when I load the sample on an agarose gel, I can...

18 May 2023 860 3 View

How to I combine 2 ligands to 1 receptor for molecular docking using autodock vina ?

I am doing my thesis for the last season of college and ı need to dock to ligand and protein for better binding affinity ı decided to combine the two ligand for moluecular docking so how can I...

28 December 2022 7,242 4 View

Should I use crystal structure of protein for molecular docking and Is ıt easiest the process ?

For the protein and ligand preparation process what kind of structure should ı choose and what is the reason of that

28 December 2022 9,166 5 View

How can I write multigroup SEM syntax in JASP?

Hi everyone, I have conducted multigroup sem in JASP. I got measurement invariance test results that I expected. Now, I wonder to know how I can write the syntax showing constrained path to be...

28 December 2022 2,457 2 View

With which formula can the metabolic energy value of silage be calculated (for chickens, especially geese). Which is the current or most valid method?

silage is forage and poultry has little benefit from it. Geese can digest roughage a little more than other poultry. Each roughage has a different degree of digestion. Therefore, the metabolizable...

10 May 2022 6,603 3 View

Is it suitable to use a density-based solver to solve supercritical CO2 laminar flow?

We have been numerically investigating the thermal-fluid characteristic of sCO2 laminar flowing in a 0.5 mm diameter circular microtube in upward direction. Depending on sharp density change along...

29 June 2020 5,332 2 View

How will affect the coronavirus mnc pop in world? Recession?

The spread of Covid-19, as the disease is formally known, is unsettling supply chains, sapping sales of some products, throwing travel into chaos, freaking out the stock markets, and intensifying...

24 March 2020 7,856 5 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

How to prepare materials before protein-peptide or protein-protein docking?

Hi all, I am conducting research on screening peptides (20-35 amino acids) with potential for treating dengue fever through protein-peptide docking methods. In the protein database, I found the...

10 July 2024 8,037 1 View

Mani Balan

Once docking process done successfully, you can find the results in the bottom panel and it it will be downloaded (as excel). From the data, you should list the ligands based on minimal binding energy (highly negative sored one is best ligand). you can open the receptor molecule in pymol and open the ligand (from the resulted ligand folder of pryx ) in the same window of pymol. Now you can analyze poses and interaction hydrogen bonds and their lengths with residues. plenty of videos are available in YouTube

Gyan Prakash Rai

https://autodock-vina.readthedocs.io/en/latest/docking_multiple_ligands.html