Can anyone suggest some good standalone programs with interactive 3d structure alignment and motif search?

More Arvind Kumar's questions See All

Can anyone suggest free program for DFT-QSAR?

Also I need to know which all descriptor needs to be calculated for carrying out QSAR studies?

01 February 2013 5,947 5 View

What can molecular dynamics say about protein-ligand interactions?

Can it say anything about changes in domains if the protein ligand interacts with only one domain?

31 December 2012 6,585 5 View

Has anyone used Autodock vina pymol plugin?

I want a detailed tutorial

08 September 2012 788 1 View

How are cells able to survive at -80 degree Celsius as all the water (80% of total volume) will freeze and volume will increase leading to lysis?

I want to know how cells can remain active after so many years at -80 or even lower temperatures. I understand that enzymes would renature after thawing but still what is the molecular mechanism?

07 August 2012 9,064 22 View

Is there any open source chemical file format converter with batch conversion module other than open babel?

I am looking for a converter which can convert 50-60 molecules from .mol2 to .mol format in one go.

07 August 2012 3,334 7 View

When using autoclave we use autoclave tape which changes color to black indicating autoclaving was successful, what is the molecular mechanism?

Why do we use tape as an indicator?

07 August 2012 8,944 5 View

What are tools available to check the accuracy of model protein structure?

I wish to know the details on how to rate the structure modeled using modeller.

07 August 2012 1,464 21 View

Protein structure prediction

With hundreds of tools for the protein structure prediction from primary sequence, can anyone provide a logical approach for higher accuracy? While there are many methods for homology based...

07 August 2012 7,021 3 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 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

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 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

I am working on my Master's thesis on the biogeography of the genus Ruagea and I would like to ask, could someone help me to check whether my result?

I created a file with my outgroup and ingroup species using Beauti, ran it in BEAST, viewed it in Tracer, and then used TreeAnnotator to create a file that I imported into RASP. Could someone...

28 July 2024 2,979 1 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

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

Which software tools are best for enhancing diagnostic accuracy in chest X-ray imaging using image reconstruction and neural networks?

I am reaching out to seek your valuable advice and recommendations regarding the best software tools to use for this research. Specifically, I am looking for software with a user-friendly...

22 July 2024 3,794 1 View

How to test multivariate outlier in STATA?

Hey all, I need help testing for multivariate outliers using STATA for my master thesis. The literature recommends the Minimum Covariance Determinant (MCD) (Verardi & Dehon, 2010). I found the...

22 July 2024 8,821 2 View

MDCI module in Orca software?

Dear Researchers, My question is associated with the "MDCI" method in Orca. Please let me clarify my question using a simple example: Suppose we are going to perform CBS extrapolation using "!...

21 July 2024 1,632 0 View

Muhammad Sulaman Nawaz

Chimera 1.6 is best for this (http://www.cgl.ucsf.edu/chimera/download.html)

Saurabh Gayali

Http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index

just try. No more words :)

Paulo Gaspar

I would suggest you take a look at Eugene:

http://bioinformatics.ua.pt/EuGene/

Lazaros Mavridis

I would suggest http://threedblast.loria.fr/