9
votes
Accepted
How can I build a protein network pathway from a gene expression quantification file?
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 ...
- 2,725
8
votes
Accepted
Why are some of the gene peptides returned by biomaRt missing an asterisk in the end?
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 ...
- 1,749
7
votes
Accepted
What does the yellow mean in this image from Virus Pathogen Resource?
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 ...
- 1,241
7
votes
Accepted
What is protein secondary structure assignment?
To make it crystal clear (and make than pun):
Assignment: a 3D structure is known and the residues are assigned a secondary structure
...
- 4,174
6
votes
Influence of pH on protein peptide mass
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 ...
- 201
6
votes
Accepted
Do any publicly available databases detail protein structure and functional domains?
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 ...
- 315
6
votes
How can I build a protein network pathway from a gene expression quantification file?
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 ...
- 9,442
6
votes
How to determine a protein's cellular location based on its sequence?
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 ...
- 4,692
6
votes
What is the origin of HIV1?
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 ...
M__♦
- 11.2k
6
votes
Accepted
BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure
The problem got solved after posting on the official BioPython repo.
Because of the processing (where some residues were removed in order to align the proteins), some consecutive residues were too far ...
- 405
6
votes
Accepted
What is the function of the heteroatoms
The text you cited mentions "input structure", so they work with structures, not just "protein sequences".
Heteroatoms = atoms marked as HETATM ...
- 1,241
6
votes
Accepted
Why do we need to find minimum energy in a protein chain?
After translation, proteins fold to achieve a specific 3D structure which allows them to perform their specific functions. The structure of a protein computationally inferred through energy ...
- 76
5
votes
Protein folding problem model for quantum computers?
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 ...
- 2,725
5
votes
Accepted
Phyre2 vs ITasser, completely different models generated
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 ...
5
votes
Accepted
How to scale the size of heat map and row names font size?
heatmap.2 is very configurable, and has options to adjust the things you want to fix:
cexRow: changes the size of the row label ...
- 861
5
votes
Accepted
How could I match atom orders between a .mol2 and a .pdb?
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 ...
- 4,174
5
votes
How to translate amino acid sequences to Nucleotide sequences
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 ...
- 216
5
votes
Accepted
On the same strand, for the same gene, can exons be overlapping?
I'm not quite sure what you're asking, but pretty much anything can happen in terms of exons and transcripts:
Two different genes encoded on different strands can share the same genomic region as an ...
- 13.5k
5
votes
Accepted
What is changed in this PDB file?
So the 'right' answer here would be for you to use a diff tool of some kind (WinDiff, or just the diff command in a Unix-like environment). That would show you the ...
- 291
4
votes
Accepted
How to select a cutoff for interaction confidence in STRINGdb?
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 ...
- 429
4
votes
How to select a cutoff for interaction confidence in STRINGdb?
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 ...
- 9,442
4
votes
Why are some of the gene peptides returned by biomaRt missing an asterisk in the end?
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 ...
- 19.5k
4
votes
Accepted
How to determine the primary Uniprot accession number from a set of accession numbers?
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 ...
4
votes
Retrieval of genomic position by using biomaRt package
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 ...
- 1,749
4
votes
If I modify a PDB file with a specific mutation, how to minimize energy?
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 ...
- 41
4
votes
Accepted
Database for proteome-wide predictions of protein structures
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 ...
- 931
4
votes
Database for proteome-wide predictions of protein structures
By far the most accurate model right now should be AlphaFold, and there are open structures across several proteomes available at https://alphafold.ebi.ac.uk/.
- 141
4
votes
Accepted
How to interpret amino acid representation
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 ...
- 2,574
4
votes
Accepted
4
votes
Calculating Isoelectric point from a multifasta file
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.
- 1,266
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