9 votes
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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 ...
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7 votes
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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 ...
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7 votes
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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 ...
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  • 1,036
7 votes
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What is the difference between Assignment and Prediction?

To make it crystal clear (and make than pun): Assignment: a 3D structure is known and the residues are assigned a secondary structure ...
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  • 3,434
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 ...
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  • 201
6 votes
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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 ...
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  • 315
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 ...
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  • 4,622
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 ...
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  • 7,022
6 votes
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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 ...
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  • 385
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 ...
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5 votes
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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 ...
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5 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 ...
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  • 7,957
5 votes
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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 ...
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  • 861
5 votes
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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 ...
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  • 3,434
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 ...
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  • 216
4 votes
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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 ...
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  • 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 ...
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  • 7,957
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 ...
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  • 19.3k
4 votes
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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 ...
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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 ...
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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 ...
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4 votes
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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 ...
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  • 901
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/.
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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 ...
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  • 2,566
4 votes
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CCP4 file to a Python 3 numpy array or similar workaround

You can use Gemmi. ...
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  • 1,036
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.
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  • 1,126
4 votes
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How do I get GO annotations for a list of UniProt IDs?

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 ...
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4 votes
Accepted

Is there any database about the abundance of proteins in urine of healthy patients?

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
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  • 1,208
4 votes

Is there a publication database or search engine offering geneID or UniProtID correlation?

I think this could be close to what you're looking for: http://glad4u.zhang-lab.org/index.php Paper: GLAD4U: deriving and prioritizing gene lists from PubMed literature It works with gene names though,...
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  • 1,378
4 votes
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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 ...
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