Multiple ligands in autodock?

More Ganesh Shastry's questions See All

How is DNA labelled with radioactive sulphur? What are the advantages of this method over radiolabelling with phosphorous?

Labelling of DNA with radioactive sulphur

07 August 2014 2,504 3 View

phage Infection

What are the Biochemical changes observed during Phage infecting bacteria ? One of them is membrane potential is anything else in the list ?? Thanks in Advance, Ganesh Shastry H M

06 July 2014 1,659 0 View

Can anyone tell me about the force involved in DNA ejection in bacteriophages?

I tried to understand both The Continuum Mechanics Model and Hydrodynamic model for DNA ejection but I cannot able to draw major differences other than the osmosis involved in hydrodynamic model....

06 July 2014 3,500 2 View

Why T4 bacteriophage tail protein in SDS resistant ?

T4 bacteriophage.

04 May 2014 9,854 0 View

How can I clone and express 3Kbp of DNA?

How can I clone 3Kbp of insert into a vector and to express the protein in E coli system?

03 April 2014 7,523 2 View

Is there any assay to detect the T4 bacteriophage ghost in the given sample other than Electron microscopy?

Detection of T4 bacteriophage ghosts

02 March 2014 1,014 0 View

What is the best minimal media for E.coli strain B 11303(ATCC)?

I have to grow E.coli in a minimal media but I don't have M9 salt to prepare minimal media. Is there any other way to make minimal media for this particular strain? Thanks in advance.

02 March 2014 8,738 4 View

Is there any other way for the preparation of T4 bacteriophage ghost other than osmotic shock technique ?

Searching for any other technique for T4 bacteriophage isolation other than orthodox osmotic shock treatment.

01 February 2014 4,860 3 View

Why did the authors extrapolate a phenotype that they experimentally proved in one bacterial strain across the whole genus of the organism?

I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...

05 August 2024 6,787 4 View

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

Seeking Software Recommendations for SELEX NGS Data Analysis?

I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed

30 July 2024 1,061 5 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

Could you try using PeptiCloud and see if it's a useful tool for biology research?

PeptiCloud (www.pepticloud.com) is a bioinformatic platform that allows researchers to organize and share their data for their projects as well as collaborate with others in one place. Through...

28 July 2024 4,762 2 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

Should the amount of DNA input used for ChIP-seq library preparation be matched between the control and experimental groups?

Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...

28 July 2024 6,938 1 View

How to determine LOD values?

I am performing fluorescence experiments using a ligand to detect metal ions. I want to determine the Lowest Detection Limit (LOD) using the formula LOD = 3σ / K. However, I'm uncertain about...

19 July 2024 1,086 1 View

Rajesh K P

Yes Ganesh, you cam do. You can find lot of video manuals in youtube. You can easily learn.

Good luck

Ganesh Shastry

Thanks.

Dr Rajesh B Patil

Why don't you use Autodock Vina intead which is know for its accuracy instead.

Best luck...

Arvind Negi

Autodock Vina is better for these things and if possible try to use in the linux ,not cygwin.

Niyaz Safarov

Why ? Regardless I like linux much more for its transparent code, file system organization, friendly user society, and resistance to fail, one must confess Autodock -Vina tandem works perfectly in pure WIndows XP(SP2 or SP3) or WIn7(needs special latest version of mgl-tools)

I agree with Niyaz. In fact in windows many tools like Discovery Studio, Pymol, Argus and so on works better. I specifically found its easy to use these tools in windows. What is important is getting the native protein (energy minimization and analyzing the issues) and optimized ligands (QM optimization suits well !!! provided it is carried out with proper basis sets). A long way to get the perfect and accurate results.

Laeeq Ahmed

You can use this Repo. It works from command line.

https://github.com/laeeq80/multi-vina