How can I find the rise per residue in a protein?

More Prasun Kumar's questions See All

Monitoring Thermal Denaturation

Hi All:Sorry for such a basic question that is bothering me for a while... The question is: Why do we study thermal denaturation of alpha helical peptides at 222 nm. I can not provide anything...

06 July 2017 7,614 0 View

G-Helix and number of residues in a helix ?

Hi All I have been trying to use "G_helix". However, I am encountering a rather strange situation: I am not able to run the command when the number of residues is less than 20 (say 19).It is...

02 March 2017 1,945 1 View

How do I calculate the angle between two vectors in 3D space using atan2?

I have two vectors in 3D space and I want the angle to be in -pi,pi. Hence intend to use atan2 in place of acos function. It will be a great help, if some body can guide me.

01 February 2017 3,998 3 View

Can someone please help with Clustering 2D dataset?

I have a matrix consisting of 10000 rows and 2 columns. I wanted to cluster my dataset into k number of clusters. I am aware of the K-mean available in MATLAB, but its clustering is based on first...

04 May 2014 746 4 View

Can anyone help with small molecules and their superposition?

I have two small molecules and want to superpose them on each other. Can somebody suggest me some command line program (Linux)?

03 April 2014 2,500 10 View

Can someone help me with my simulation of Fe2+ ions and protein?

Hi all, I have to run a simulation using GROMACS, which has Fe2+ ions. In GROMACS, the C12 and C6 values for Fe are not defined. Can anybody help me in this regard? Any article or relevant data...

02 March 2014 6,541 10 View

Is there any software available to identify the central strands and end strands of a beta sheet?

Is there any software available to identify the central strands and end strands of a beta sheet or to identify the parallel and anti-parallel beta sheets?

07 August 2013 8,212 2 View

How can I prepare virus for a TEM or SEM imaging?

I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?

11 August 2024 3,115 1 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 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

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 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 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

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

How to understand this crystallographic phenomenon of low temperature crystals in zeolite?

During low-temperature testing, new diffraction peaks that appear could be indicative of several phenomena. In one of our tests, we observed notable new peaks around 40° and 45° in a specific...

06 August 2024 726 3 View

Conrado Pedebos

I believe that the g_helix tool from the GROMACS simulation suite is able to do that, as long as you have a .pdb file.

Prasun Kumar

Thanx for the reply.......For the helix even HELANAL-Plus does the correct calculation, but the real problem arises when the segment is strand (though strand is considered as helix) or loop.....Any suggestion for this........