8

I suggest you take a look at rna-pdb-tools we do way more than you need! :-) The tools can get you a sequence, secondary structure and much more using various algorithms, and all is well documented http://rna-pdb-tools.readthedocs.io/en/latest/ To get sequence http://rna-pdb-tools.readthedocs.io/en/latest/main.html#get-sequence $ rna_pdb_tools.py --...


6

Some of this information (at least some domains, active sites, etc) is available from UniProt. If you want to download their whole database, you can search without specifying any terms and then click the Download button.


5

OK, I got an answer here. Use: frank off to get:


4

Context The PDB file format is a fixed-column file format designed in 1970s for storing structural models of macromolecules. The format has been around for long time, has many uses, and although it has official spec the files in circulation may not strictly conform to it. It always has a list of atoms with coordinates (the first two lines are added to ...


4

For the first question: "how many of long non coding can make hairpin loop structure?" The easiest thing to would be to run your sequences through an RNA secondary structure prediction tool. There's a few tools for doing this but the most commonly used are RNAfold from the ViennaRNA package and mfold. This will give you an output that looks like this, ...


3

To add a more complete answer: the current coronavirus is closely related to the SARS virus that caused the outbreak in 2004, and on which much research has been done. Here is a general review of the coronavirus epidemiology, life cycle etc. I haven't found yet any materials about the RNA structures in the translatable region, however the structures in the ...


3

Please look up flavivirus 'double loops' as you described them previously (post for "Coronavirus RNA') and associated RNA secondary structure anomalies for dengue virus and associated vaccine (Butantan) and the yellow fever virus and its vaccine (17D). If you are aware of "double loops", we must be aware of the association of RNA secondardy structure and ...


3

EnsEMBL also has this. Search for your gene of interest, choose your transcript, go to the page of its protein product(s), and select "Domains & Features" from the right-hand menu (using human p53 as an example): Domain source Start End Description Accession InterPro PANTHER 3 331 - ...


2

Ok, the answer was right here and I missed it, posting it in case anyone else will do the same mistake as me in the future. U = unpaired P = paired H = hairpin B = bulge I = internal loop M = multiloop S = stem (or stack) E = external loop


2

Excellent question! I would recommend that you start with an NIH resource at the National Library of Medicine (NLM). PubMed (https://pubmed.ncbi.nlm.nih.gov/) provides search capabilities across the biomedical literature. You can also create an account and use it to manage your searches of the literature. An example search below for "protein misfolding ...


1

If you know how to use python: 1 - Download the ModeRNA module from here and install 2 - from a python IDLE execute: from moderna import * m = load_model('file.pdb', 'A') #A is the chain seq = m.get_sequence() sec = m.get_secstruc() the variable sec store the secondary structure in dot-bracket notation.


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