Is it reliable to use AutoDock for docking quite long RNA molecules to protein structures?

More Abdalla G. Alia's questions See All

Is it necessary to covary exogenous constructs in a structural model?

I am working on a SEM model where i have 7 latent variables (6 exogenous and 1 endogenous). In AMOS when I co-vary the exogenous constructs, only 2 paths are coming significant out of 6. But when...

03 August 2024 6,028 4 View

What are the names of journals in animal nutrition rated free and fast publishing journals?

Animal Nutrition

20 March 2024 6,218 0 View

How to get the band.dat (band) files in phonopy calculations using VASP?

Hello Dear All I am a new user of VASP (Vienna ab-initio simulation packages) and tried to calculate the phonon using VASP. I get the phonon band structure (after calculations) in image form(.png...

11 December 2023 9,204 6 View

I would like to read about Technology or ICT integration into Pre-service Teacher Education, would you please recommend some books?

It can be books, papers, articles... I will read it for a literature review.

25 August 2023 3,659 9 View

Inquiry about secondary metabolite compounds production in specific bacterial strain?

Greetings everyone. During my master's research, I focused on exploring the potential of a specific bacterial strain to produce antibacterial compounds. To achieve this, I used the technique of...

24 August 2023 588 4 View

You are given the following cost data?

You are given the following cost data: Total fixed costs are 100. Q= 0,1,2,3,4,5,6 TVC= 0,5,10,20,40,65,95. Where Q=Quantity and TVC=Total Variable Cost Required a) If the price of output is...

30 July 2023 3,858 1 View

How to check immunogenicity and cytotoxicity of a drug delivery system like PLGA/PEG using in-vitro methods?

Background: I am working on checking the in-vitro immunogenicity of a molecule encapsulated in a PLGA (microspheres) drug delivery system. After the addition of the drug to the cells, I observed...

12 July 2023 6,139 0 View

Call of Editorial boards at Algerian Journal of Biosciences?

Call of Edotrial boards in Algerian Journal of Biosciences About more informations please visit the journal website https://www.journal.acse.science/index.php/ajb/index If you are interested...

17 April 2023 3,999 0 View

Is it possible to detect PAHs directly from microplastic particles found in fish guts and gills?

I have already processed my fish gut samples for microplastics analysis from extraction to filtration and drying. The extracted microplastic particles were stored in dried glass fiber membranes....

16 April 2023 8,457 2 View

Stock solution of α-Amylase Porcine Pancreatic powder (Megazyme)?

How to prepare a stock solution of α-Amylase from Porcine Pancreatic powder from Megazyme with an activity comparable to a 1000U/mg stock solution of α-Amylase from Porcine Pancreas from...

29 March 2023 3,397 0 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

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 View

How to add Cr parameter in autodock?

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!

29 July 2024 488 0 View

How to retain the a GFP tagged gene expression in stable cell line?

Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....

29 July 2024 5,007 0 View

What is the relationship between protein structure and N or C terminal tagging choosing?

I want to do 2,3-butanediol dehydrogenase(BDH) enzyme purification to confirm its activity for 2,3-butanediol. Before that, I need to confirm which N or C terminal tagging is better for enzyme...

28 July 2024 366 3 View

Why cannot i find my protein on cell surface after antibiotic selection of expressing plasmid?

I cannot confirm cell surface protein expression by flow cytometry even after transfection and antibiotic selection of cells. Does it take long for proteins to express on the cell surface? the...

28 July 2024 3,178 3 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

EDC carbodiimide and NHS easter 's half life among different pH?

It has been long known that EDC carbodiimide and NHS easter's half life agains hydrolysis are highly related to pH. However, very surprisingly, not yet found a paper giving a table/chart of their...

25 July 2024 8,738 0 View

Martiniano Bello

HDOCK is more suitable to protein-rna docking calculations.

https://academic.oup.com/nar/article/45/W1/W365/3829194

Abdalla G. Alia

Martiniano Bello Thanks for your suggestion!

Uttam Pal Thank you for your answer and suggestions. I agree with you regarding the reliability of molecular docking results. However, it does give some indication and enrichment.