During Glide docking of siRNA with a protein using Maestro 2020-3 what steps should I follow for the proper preparation of siRNA?

11 June 2024 0 6K Report

How can I perform Glide docking of siRNA with a protein using Maestro 2020-3? Despite modeling and validating my siRNA, the docking process fails to generate the out.maegz file, preventing me from obtaining a Glide score. What steps should I follow to ensure successful docking and score generation?

Badges
Science method

More Ive Sultana's questions See All

How to generate electron density map in GSAS II software?

I would like to learn the procedure for generating an electron density map using the GSAS II software. I previously saw suggestions, but I am unable to execute them. I would really appreciate any...

17 March 2024 4,555 2 View

Reference mapping and de novo algorithm for genome assembly?

Hello, I am working on viral metagenomics and have started using the High Throughput Sequencing reads for virus genome assembly. Since, I am at the beginner level, I have some confusions. As these...

01 February 2024 296 1 View

Can anyone tell me the procedure of dissolving SnO2 into hot aqueous solution of hydrochloric acid?

I want to dissolve SnO2. But as it is not soluble in water, I need to add this in hot aqueous solution of strong acid. For that, I need to know the temperature and time parameter required for...

27 January 2024 1,232 0 View

Site Response Analysis by PLAXIS 2D and 3D?

Does anyone know how to plot Depth Vs PGA graph in PLAXIS 2D and 3D?

15 January 2024 2,224 0 View

Can I publish my research paper here ? what are the guidelines ?

10 December 2023 1,167 3 View

How can we determine final concentration from calibration curve for same concentration for kinetic studies?

We have to find equilibrium concentration from calibration curve for same concentration for effect of contact time and kinetic studies using uv vis. There won't be any slope for just one initial...

20 October 2023 909 0 View

Can adsorption isotherm be calculated from 3 initial concentration for heavy metal removal?

We have taken 10 g/l, 5 g/l and 2.5 g/l as initial concentration. And calculated concentration equilibrium from absorbance uv-vis spectrometer. So 3 concentration will be enough for adsorption...

16 October 2023 5,725 2 View

Which adsorption isotherm would fit more?

The values of the correlation coefficient of biosorbent estimated for langmuir and freundlich isotherm were both high 0.99908 and 0.99994 accordingly. But 1/n value were not between 0 to 1 for...

16 October 2023 1,075 3 View

How can I remove too many small bubbles formed after homogenizing my starch film forming solution?

I have tried ultrasonication using Branson digital sonicator- 10 mins, 10% amplitude.

26 September 2023 6,865 1 View

How can I do energy decomposition analysis (EDA) using gaussian g09?

I need to do energy decomposition analysis for my molecules. Is there any free software with which I can perform this job? I am using windows and not familiar with linux environment. Any...

30 July 2023 3,618 2 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 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

Optimal siRNA Volume for Complexation with Liposomes in a 2.5 mL Solution with 10 mg/mL Lipid Concentration?

How much volume of siRNA can I add to 2.5 mL of liposomes with a total lipid concentration of 10 mg/mL?

27 July 2024 6,920 1 View

Why my negative control siRNA is decreasing the target gene's expression?

Hi Everyone, I'm using an siRNA kit to knock down a target gene. The kit guarantees that the negative control doesn't target any sequence in mouse genome, and when I use BLAST I don't find any...

23 July 2024 2,673 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

Optimal siRNA Volume for Complexation with Liposomes in a 2.5 mL Solution with 5 mg/mL Lipid Concentration?

How much volume of siRNA can I add to 2.5 mL of liposomes with a total lipid concentration of 5 mg/mL?

18 July 2024 9,831 0 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