How can i calculate secondary structure propensity of amino acid sequences with values in percentage?

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How to succesfully simulate protein-RNA complex in excess salt concentration using gromacs?

I want to simulate a protein-RNA complex in a salt concentration of 150mM. I neutralised the charge of the system by adding 14 Na+ ions and followed that by adding extra salt concentration using...

03 April 2019 1,778 2 View

How to determine the box dimension for umbrella sampling?

I am using Gromacs 2016 to do umbrella sampling of a protein-RNA complex. I am following the Lemkul's tutorial of umbrella sampling, but I couldn't get how the box dimension was determined. For a...

03 April 2019 501 8 View

How to simulate RNA using GROMACS package with amber99sb-ildn forcefield?

I have a modeled structure of RNA with 25 nts. I have renamed the atoms as per the rtp file of the amber99sb-ildn force field. All the steps upto energy minimisation ran without any error. The...

10 November 2018 7,721 3 View

How reliable is a modled RNA structure for further docking and simulation study?

I have a 30 nucleotide long RNA sequence, the binding of which I wanted to study with a protein (which has crystal structure available). I am trying to model the RNA structure and further use it...

07 August 2018 9,491 2 View

How to seggregate RNA bound proteins from a list of pdb files?

I have a dataset of pdb files which are all complex structures. From them, I have to select only those which are protein-RNA complexes. I code in python. I am trying to use a keyword or pattern to...

09 October 2017 996 2 View

What is the preffered force field for an idp-RNA complex simulation?

For protein-RNA complex, amber ff14SB works good, but am not sure if this forcefield will be ok to use for a disordered protein complex. Pl. suggest the optimum choice of forcefield and the...

10 November 2016 9,066 7 View

Can anyone help me with pepdata package of python, want to use it for amino acid properties?

I have installed the package but cannot understand how to use the functions for amino acid properties for my given set of sequences.

09 October 2015 1,867 3 View

How to find if a pdb file is having complex structure or unbound structure?

I have a set of pdb files which I have to seggregate into monomer, dimer (homo+hetero) and protein-nucleic acid. Kindly help with the keyword to look for, I shall write my code accordingly. Thanks...

01 January 1970 7,803 4 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

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

Is it possible to plot the atom-projected band structure using GPAW?

Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...

07 August 2024 269 3 View

Separation of organic acids-HPLC?

Hello What should be done to separate and identify organic acids in HPC when their RetTime is the same?Like oxalic acid with Propanoic Acid.or acids that have a very close RetTime.

07 August 2024 8,782 3 View

The aqueous fraction of the hydroethanolic extract is showing the presence of palmitic acid. What is the mechanism responsible ?

Palmitic acid presence in aqueous fraction

05 August 2024 8,624 4 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

How to convert g/kg Humic acid dose to kg/ha?

I used humic acid at 0.044 g/kg soil in my pot experiment. But finally, I have to recommend kg/ha. Each pot's soil weight was 11 kg. What is the solution?

02 August 2024 7,186 6 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,079 0 View

Conjugation of PEG-Amine to an Amino Acid Using EDC?

I am attempting to conjugate PEG to an amino acid at the C-terminus, for the purposes of producing nanoparticles. I have been told that PEG modified with amine groups can be used for this purpose,...

31 July 2024 2,033 1 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

Mangal Singh

You can try GOR

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html

Sushmita Basu

Thank you so much. It helped.

Prasanna Premadasa K M Gamage

Freq of aa in Helix/ Freq of residues to be in Helix

use Ab initio (Chau fasten/ GOR) or Homology based (nearest neighbour/ neural network) methods