Can any one recomend me a software construct a desired DNA strand, please do not recommend me 3D Dart..

More Ashfaq Ahmad's questions See All

How can one simulate protein with a Copper ligand in NAMD?

Hello Everyone, I want to use NAMD to simulate transemembrane protein with copper as a ligand. Can anyone guide me how to fix the following issues; 1. Do I need to dock copper to my protein first?...

31 December 2014 5,517 3 View

How this paper can be discussed, as almost every paper is agreed on coupling mechanism from structure labs and NMR labs?

Indeed you have answered in a very beautiful way and provide sufficient data but my question is that what could be the possible explanation, i did not find any good in your discussion section.

11 December 2014 1,801 0 View

Can anyone advise on protein stitching?

I want to stitch two different proteins. My next step is to generate my data using HHblits server. By putting both the proteins in one sequence, HHblits will only result in one part and will...

10 November 2013 2,654 4 View

Does anyone know about protein sequence stitching?

I want to stitch two different proteins in one sequence so that blast can read it thoroughly. Any one of you in this community has any experience or idea about this?

10 November 2013 1,022 0 View

Write your research proposal, following some easy steps

03 April 2012 6,844 2 View

http://expertscolumn.com/content/silver-staining-protocol-stain-sds-page Protocol of silver staining of SDS-PAGE gels, I used it personally and it wo...

http://expertscolumn.com/content/silver-staining-protocol-stain-sds-page Protocol of silver staining of SDS-PAGE gels, I used it personally and it worked very well. Silver staining is much more...

02 March 2012 6,830 0 View

Six steps to win international scholarships

02 March 2012 4,240 0 View

Six key steps to win international PhD scholarships

02 March 2012 7,785 0 View

protocol for silver staining SDS-PAGE.

02 March 2012 4,675 0 View

Here is a silver staining protocol for your SDS-PAGE. Cheers,

02 March 2012 6,338 0 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

Who will be moral responsible for the death of thousands of people in the event of an earthquake?

Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...

08 August 2024 6,134 12 View

Are there any instruments for studying time similar to the way it is in space?

There are a huge number of methods for studying objects in space, according to the senses (and not only). Mechanical, thermal, optical, acoustic, electrical, magnetic, based on particle beams,...

06 August 2024 7,102 0 View

Weak DAPI staining after immunohistochemistry - how to improve?

After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...

05 August 2024 9,637 2 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

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

05 August 2024 6,247 3 View

In the case of a wound l recurrence after radical breast cancer and sentinel lymph node biopsy. Are the sentinel lymph node procedure recommended?

In the case of a wound l recurrence after radical breast cancer and sentinel lymph node biopsy. Are the sentinel lymph node procedure recommended? If no axillary lymph node dissection was not...

05 August 2024 8,056 1 View

Regarding a model for simulating battery charge and discharge, what do you consider to be high fidelity?

Regarding a model for simulating battery charge and discharge, what do you consider to be high fidelity? What is the acceptable percentage of error (regardless of the metric)? Could you suggest...

03 August 2024 5,358 0 View

Interested in a SCOPUS collaboration?

Hi RG family. My team and I are working on some SCOPUS publications and we need co-authors who are willing and capable of undertaking both qualitative and quantitative-based studies. The scope...

02 August 2024 7,843 0 View

Pierre Pétriacq

You may use ApE : http://biologylabs.utah.edu/jorgensen/wayned/ape/ but I am not sure of what you are looking for exactly

Ashfaq Ahmad

I need to construct particular region (protein binding) of S. mutans DNA. In the next step i am trying to dock helix-turn-helix (HTH) a DNA binding region of a response regulator. I have used vina for protein docking, but this is will be a new kind of test for me because i never tried protein DNA. I checked out 3D-DART to construct DNA strand using a template from PDB but the software is unable to do so in my case. So i wish for some another program to construct my DNA strand and complete my first step. Thanks Pierre in Advance

Andries Zijlstra

Try Geneious. Its rapidly becoming one of the most mature software packages that don't require intense knowledge of the command line.

Thanks for referring geneious, but Geneious is unable to model DNA, or dock protein DNA. The program is good for an undergraduate student who wish to learn the ABC of computational biology.

Yejun Wang

You could try VectorFriends at http://www.vectorfriends.com

It’s free for academic researchers