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

More Sushmita Basu's questions See All

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 391 8 View

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 1,593 2 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 7,564 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 9,358 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 880 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 8,951 7 View

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

I have 27 sequences of varied length (20-600) for which i need to know the secondary structure propensities.

08 September 2015 3,897 4 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 7,662 4 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Chlorinated organic formation in odor control scrubbers using hypochlorite?

I'm involved in a study of odor control technologies for municipal wastewater treatment plant. One of the control options involves a chemical 2-stage (acid/alkaline) packed bed scrubber. The...

03 March 2021 3,661 2 View

What solvent can I used for Paal Knorr reaction between 6-amino hexanoic acid and 2.5 hexanedione?

I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...

02 March 2021 4,443 2 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Ester cleavage conditions?

Hi all, I need to cleave the ester in Ethyl 2-amino-1H-imidazole-5-carboxylate to make the carboxylic acid and retrieve the product from solution to use in downstream applications of linking to...

01 March 2021 8,766 3 View

How to define and get results (stresses) for certain points of a model in abaqus, using python? When the size of the model changes?

I want to do a parameter study of a aixsymmetric cylinder in Abaqus. I want to create several jobs where I get the stresses for 3 different points in my model. These points are defined. I wrote a...

01 March 2021 10,078 1 View

Which is suitable for use with Python? MySQL or SQL Server?

Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?

01 March 2021 3,422 3 View

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....

01 March 2021 3,607 3 View

How to remove DCU and HOBT from my reaction?

I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??

28 February 2021 2,153 1 View

Can anyone provide the Support vector regression code structure of LIBSVM MATLAB or python ?

Please, if Gaussian Parameter optimization is possible in this code structure

28 February 2021 278 3 View

Taher Ahmed Ghaleb

There are some typical examples on how to calculate amino acid properties in Biopython.

For example, here is some python code for calculating some of these:

http://biopython.org/w/index.php?title=ProtParam&redirect=no

This database: http://www.genome.jp/aaindex/ has also many of the propensity scales.

All the best.

Sushmita Basu

Thank you. I shall try doing it using biopython.

Good luck.