7

I looked for relevant publications at Web of Science using 'structur* AND cyclodextrin' in the Title field. For the period 2011-2012 there were 56 hits including: Racz et al (2012) Structure of the inclusion complex of beta-cyclodextrin with lipoic acid from laboratory powder diffraction data. Acta Crystallographica Section B 68: 164-170 Ali et al (...


5

Have you used hhpred to search for homologues? What was your criteria for defining there was no homologues? You could potentially go down to around 30% sequence identity to model. I would submit the the query sequence to both I-Tasser and Rosetta and see if both of the servers agree on the topology. I-Tasser will always provide 5 models of your query ...


4

B-form DNA is wrapped around histones in a left-handed manner resulting in a left-handed solenoidal superhelix (see that, that and this). The reason for this wrapping is that it reduces the helical tension. This post has more information about DNA helical tension. Also note that exceptions exist (i.e. right-ended direction) especially for histone at the ...


3

3D structure. Use the PDB to identify structures that are similar to the one you have found (you can use BLAST to search the PDB). A 30% match or above is usually acceptable, and multiple alignments are of course useful at lower match scores. If structures exist that are similar enough, you can use homology modelling to generate a 3D structure (this is what ...


3

You can use R-coffee of the T-coffee suite of tools. In general, the *coffee tools are excellent and work very well if you can get over their author's self obsession1. R-coffee can align RNA sequences taking into account structural information: 1 The guy actually adds his name to the output of all his programs! Seriously, he does. Apart from being simply ...


2

there a number of tools in the Vienna package (RNAalifold, RNALalifold): http://www.tbi.univie.ac.at/~ronny/RNA/index.html some other tools are available from Freiburg Univ. such as: LocARNA or CARNA (http://rna.informatik.uni-freiburg.de/CARNA/Input.jsp)


2

I frankly don't trust Mfold or RNAfold for finding structure. There are just too many false positives and without experimental verification, it's not reliable. For finding hypothetical local structure, it's great. However to find evolutionary conserved structure MSA methods like what has been used with Rfam are a more suitable way. Since you asked for ...


2

Swiss model is an online tool for modelling protein tertiary and Quaternary structure using evolutionary information. J-pred and Swiss model both are pretty straight forward tools which requires only the sequence. Swiss model requires searching for a template and based on which the protein will be modeled further.J=pred is exclusively used for secondary ...


2

Yes, the structure predicted by splitting up the sequence may not represent the actual structure of the full-length RNA. A simple hypothetical case would be that of an RNA whose 3' and 5' UTR interact to cause circularization. I am afraid there is not clear rule for choosing the subsequences such that the assembly of the individual secondary structures is ...


2

The question asks why the distribution of coil, alpha-helix and beta-strand is 60:30:10 rather than 33:33:33. The answer is: “Why not” This is because there is no reason whatever to expect that three types of structure (or in the case of coils, lack of structure*) should be present in equal amounts in proteins. It is like expecting that the percentage ...


2

As Martin pointed out, VMD doesn't update secondary structure content over the course of an MD trajectory. You can easily do this in VMD by using the SSCache script: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/sscache/sscache.tcl I believe it ships with the newest versions of VMD, actually, but I'm not exactly sure; even if not, you can ...


1

From comments I understood that you need to predictions in bulk. You can use API based system of JPred. They allow you to submit more than 1000 jobs per user per day. You can go through instructions step by step from their documentation. It looks simple ! Another hit I got while searching is Phyre2. I am sure there are many such servers.


1

I suggest you to use modeller - advance modelling (https://salilab.org/modeller/tutorial/advanced.html), Where you can use multiple template PDB to get final model structure. All the best..:)


1

There is no hard and fast rule for how many nucleotides you have to select. If your miRNA is ~20nt and you take 70nt from both sides (average length of hairpins is ~84nt in humans), your total length will be 160nt. The point of taking $\pm70nt$ is that you don't know if your read is -3p or -5p. So take 70nt from both sides. The maximum length of a human ...


1

There won't be any duplicates in miRBase (for a given organism). Choose the taxon nearest to your organism if you are doing homology based discovery. If you want to take all/many organisms then you can use fastx_collapser to collapse redundant sequences. However you will lose the name of the miRNA. You can use awk also for this and it will keep the sequence ...


1

The green region will definitely not make an miRNA: It is not a part of a stem loop. See typical miRNA structures from miRbase. EDIT Bulges can sometimes determine which strand is chosen as mature miRNA. However, this green region is also is unlikely to form miRNA because the stem is just 15bp.


1

I think your suggestions are fine - there are a few ways you could write this. I might use some variant of; The techniques used may be specific to the research question, and particular considerations may also be required depending on the accepted norms within the academic field


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