9

There are multiple ways to do this, and multiple protein interaction databases besides the ones you mentioned, such as BioGRID or IntAct. Interaction databases are different in how interactions are defined, sometimes it can be experimental evidence of interaction, sometimes coexpression, orthology-based predictions, etc. There is no single solution to your ...


7

If it's 3' incomplete that means the evidence used to create it was a fragment. Here's the evidence used to construct BRCA1-214 ENST00000477152.5, a 3' incomplete. You can see that there's a full length cDNA from EMBL, AK307553.1, which was used to create this model. The sequence was mapped against the genome sequence to create the transcript model. When ...


7

To make it crystal clear (and make than pun): Assignment: a 3D structure is known and the residues are assigned a secondary structure Prediction: an algorithm predicts from linear (primary) sequence what the secondary structure may be —often incorrectly. This can be homology based, covariance, deep learning etc. But most commonly just the vector norm of ...


6

Your approach in general seems to be OK, but I have a few suggestions: You are basing all your calculations on whether the pH is above or below 7. However the N and C termini have pKa values that determine whether these groups will be ionized (8 and 3, respectively). You should check whether the pH is above/below these values instead of 7. Different amino ...


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.


6

You could use Blast2go to find the predicted relevant gene ontologies of your sequences. If you look for the cellular compartment sub ontology you should find the location of such protein. I have never used this tool, but here is the paper describing how it works. I wouldn't restrict to the first predicted match of blastp see if some more genes with a good ...


6

Sulfur atoms are shown in yellow. The molecular viewer that you use is JSMol (JMol ported to the web). Atoms are colored by element: grey C, blue N, red O and yellow S. If you wonder how other atoms would be colored, see JMol's Default element colors, by periodic table.


5

Protein folding problem can be viewed as a minimization problem. One can use quantum annealing to perform the minimization. Running this on quantum computers would improve the performance since they can perform the tunneling directly. In fact, quantum annealing was used (blog post) for lattice protein folding on the the D-Wave quantum computer (128 qubits). ...


5

I'm less familiar with Phyre, but I-TASSER is a really sophisticated system that takes the results of a search using multiple threaders and plugs them into an ab initio simulation which tries to minimize the energy of the models by sampling many possible 3D conformations, which I don't think Phyre does. https://en.wikipedia.org/wiki/I-TASSER#/media/File:I-...


5

Many interaction databases now work with PSI format files. Most of the main databases can do this and the EBI has set up PSICQUIC View, a very useful page where you can query multiple databases at once. Note that it is very important to limit the results according to the detection method. There is a lot of noise in protein interaction databases. Depending ...


5

heatmap.2 is very configurable, and has options to adjust the things you want to fix: cexRow: changes the size of the row label font. keysize: numeric value indicating the size of the key. The size of the key is also affected by the layout of the plot. heatmap.2 splits your plotting device into 4 panes (see the picture below), and you can control the ...


5

Atom reordering is a common problem in compchemistry. Rdkit (a python package) can do this, but it is limited by the formats it can read and mol2 files are a bit hit or miss. It works really well with SMILES, SMARTS and mol (sdf) files. But the writing may cause problems with Brookhaven pdb and mol2 files. So the formats you have are both problematic. One ...


5

Although there is not a unique nucleotide sequence that translates to a given protein, one can list all the possible DNA sequences that do translate to that protein. An online tool that does just that is Backtranambig, from EMBOSS. It produces a DNA sequence representing all the nucleotide sequences matching the input protein, using IUPAC ambiguity codes.


5

They are both lentiviruses and share a distant common ancestor. HIV-1 and HIV-2 are descendents from simian immunodeficiency virus (SIV). The following tree shows the relationships very clearly, from Wertheim and Worobey (2009) Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2 PLoS Comp Biol. here. The evolution of HIV-1 is heavily mixed ...


4

I have used STRING pretty heavily, and have compared it to various other databases of protein interactions and signaling pathways. I do feel like it has a lot of quality interaction annotations, but you have to sift through a lot of noise to get to them. The simplest method I have found for doing this is to look at the individual scores for each ...


4

This depends on what you are trying to do and whether you value specificity over sensitivity. We can't tell you since it is entirely dependent on the biological question you want to answer. However, I would recommend two things: Don't use STRING. The creators of STRING made the choice to value sensitivity over all else, so they include any interaction they ...


4

If you look at the original data at Ensembl you'll notice that most of these are labeled "CDS 3' incomplete" and have a TSL (transcript support level) of 1, which is as low as it goes. It seems likely that that is simply an incomplete annotation. I'm not surprised that there are a bunch of these for BRCA1, since there was a long time when there were a LOT of ...


4

Reposting my answer from the related ticket in the Biology section: I think there is an issue with the terminology. The "primary" accession number, is the first accession number in cases where an entry has more than one accession number, as described in http://www.uniprot.org/help/accession_numbers: Entries can have more than one accession number. This ...


4

BiomaRt cannot do that I'm afraid. There is an Ensembl REST API endpoint that will get you the genomic location of protein coordinates. It needs an Ensembl peptide ID an input though, so you could use the xref endpoint first to get that. There's a bit of sample code in R on those pages, you could use that to script together if you've got a list of these.


4

Yes you can modify the reference PDB file and look for the changes and for this purpose you need visualizers. One among these is Chimera. You can easily carry out the energy minimization steps using Chimera, first mutate your PDB file manually and then provide it as an input for Chimera and the steps for doing energy minimization are fairly simple as given ...


4

There are three initiatives I know of to have a go at this: PConsFam, which collects data from this paper. The Baker group's metagenomic study which you mention in the question. The recent DMPfold work from our lab. This compares its results to the above two studies and discusses the effect on various model organisms. The second and third of these don't ...


4

This means that at position 383 the Cysteine(C) is mutated to a Serine(S). Depending on the organism and gene usually the mutation notation is linked to a specific transcript since the position could vary depending on transcript splicing.


4

You can use EMBOSS Pepstats for this. It takes a multi-fasta as input and produces a table that contains various statistics related to the protein, including isoelectric point.


4

The link to the FTP for the GOA database files is listed on the GOA Downloads page. The file containing the mapping info you seek, goa_uniprot.all, comes in two formats, .gaf and .gpa. The README in the FTP directory linked provides details on the structure of the files. Below is the first 20 lines of the .gaf file after uncompressing. Column 2 contains the ...


4

If you have access to the UK Biobank dataset, then they have urine data for healthy individuals. https://www.nature.com/articles/s41588-020-00757-z


3

Consider the circumstances in which entries will have more than one accession (taken from the same page you linked in the original post). Entries will have more than one accession number if they have been merged or split. For example, when two entries are merged into one, the accession numbers from both entries are stored in the AC line(s). If an existing ...


3

I guess you already know what identity means. But for completeness, it is the % of pairwise alignment position which have an identical amino acid residue. For the identity+similarity it is important to know that amino acids can be grouped according to their physicochemical properties e.g. charge, size etc. While there are standard groupings for amino acids ...


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 - ...


3

Amino-acid content (eg Lys, Asp) can have drastic effect on observance in a particular MS-mode. You should consider including Peptides::pI() or Peptides::charge() to determine the likelihood of (de-)protonation in your calculations.


3

Another quick Google search reveals the Peptides R package. library(Peptides) s <- "RKTTLVPNTQTASPR" charge(s) [1] 2.997683 Optional arguments to charge() are pH (default = 7) and pKscale (choice of nine, default = "Lehninger"). See ?charge for details. Another (non-R) option is the EMBOSS suite program iep. I highly recommend installing EMBOSS, it ...


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