Stack Exchange Network

Stack Exchange network consists of 174 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

Questions tagged [proteins]

Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.

1
vote
1answer
25 views

De novo motif discovery in protein sequences

I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a ...
0
votes
0answers
10 views

Finding the conserved region of protein in a given set of Kingdom

We have to find the conserved region of proteins in a given set of kingdom and we have to give more weightage to distantly related organism. What approach I should take to solve this problem?
1
vote
1answer
49 views

API/website for blasting peptide sequence against database of all plant proteomes

I would like to blast a peptide sequence against all available plant proteome databases, i.e. a blastp metaproteome analysis. What tools are available? Which ...
2
votes
0answers
85 views

Searching for start and stop codons for protein sequencing of contigs

I need to convert contigs into their respective protein sequences given a reference genome (i.e. I need to take a substring, whose position is already known on the string, and I need to locate the ...
-1
votes
1answer
36 views

How to calculate Gene Ontology terms in python

I am testing different Protein-Protein Interaction networks alignment tools. I observed that all alignment tools show some ...
2
votes
0answers
35 views

How to assign the best gap penalty and gap extension penalty using BLOSUM65

For an assignment I must do a pairwise optimal local alignment using BLOSUM65 and five protein sequences. The algorithm I want to use is the Smith-Waterman. Context protein sequencing using Blastp: ...
1
vote
1answer
17 views

How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?

Given a normal protein sequence with the 20 standard amino acids, how can the 'Autocovariances', 'autocorrelations', and 'autocorrelation coefficients' of the sequence be calculated? What is meant by ...
1
vote
1answer
73 views

Extract certain fields using from GenBank file using Bash script

I need to extract certain lines from a GenBank file on Linux. Input file: ...
2
votes
3answers
66 views

How to get the product of a CDS

I need the name of the protein in /product="protein_name" using bash commands. Beware, there is a lot of whitespace between lines. ...
2
votes
2answers
46 views

Genomic coordinates of predicted binding pocket

I would like to know the genomic coordinates of a proteins ligand-binding pocket. For example, on this PDB page you can see that there is xray crystallography data for how CYP2C9 interacts with two ...
0
votes
0answers
32 views

Buried Protein Atoms vs. Solvent-Accessible Protein Atoms

I am trying to come up with an algorithm that would differentiate solvent-exposed surface atoms from cavities which can fit water inside. Unfortunately, it seems the Shrake-Rupley algorithm does not ...
0
votes
1answer
33 views

How to calculate Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation from protein (amino acid) sequences?

I want to code Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation in Python 3.6 from the scratch for amino acid sequences without using any package. Unfortunately, I have not ...
1
vote
1answer
30 views

Which is the amino acids classification when analyzing the solvent accessibility of a protein?

I came across an article which has defined 3 categories: Buried [A, L, F, C, G, I, V, W], Exposed [ R, K, Q, E, N, D] and Intermediate [M, S, P, T, H, Y] when analyzing the solvent accessibility of a ...
1
vote
2answers
404 views

How to scale the size of heat map and row names font size?

I have an expression data matrix (120X15; 15 samples and 120 genes), my heatmap looks blurred and raw names (gene names) looks very small and can not read. How can I improve my scripts? Here is the ...
0
votes
0answers
17 views

What is the most efficient method to identify a protein that has undergone post-translational modifications by an enzyme?

I am in the process of conducting research on a wide array of proteins that are all post-translationally modified by the human enzyme GSK-3beta. What is the best to show (using peer-reviewed research ...
2
votes
1answer
64 views

Download proteomes from NCBI based only on binomial names

I'm trying to download around 2000 proteomes from NCBI, but all I have is the genus and species e.g: lophodermium_seditiosum trichoderma_harzianum Does anyone know ...
3
votes
1answer
43 views

Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms

I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms. Specifically, I'd like to determine the ...
1
vote
1answer
36 views

Label protein strucuture residues in Chimera

I have generated proteins structure of capsid protein of two strains of viruses. I have modeled them showing Columbic electrostatic potential. I have opened them in two separate windows for comparison....
0
votes
1answer
23 views

Automating download of results of Drug and Drug Target Mapping

The drug and drug target mapping tool shows the top 3 PDB IDs for each drug based on the drug target sequence similarity search and ligand id search. Is there a way to get all the PDB ids of the drug-...
4
votes
2answers
56 views

If I modify a PDB file with a specific mutation, how to minimize energy?

I have a series of proteins that are all phylogenetically related. Only one of this proteins is currently X-ray crystallized. Is it valid to modify the reference PDB file (I mean by hand) to match ...
1
vote
0answers
61 views

How to predict the distance between two residues in a protein sequence

I have some protein sequences and I need to predict the physical distance between each two residues in the protein when folded correctly in 3 dimensions; I need to predict this distances just by ...
2
votes
2answers
48 views

Protein expression units?

I'm starting for protein expression analysis. In gene expression, we have TPM, RPKM etc. However, all I can see for protein expression is: "High", "Medium", "Low" and "Not detected". https://www....
3
votes
1answer
60 views

Retrieval of genomic position by using biomaRt package

I have a list of several protein names, their primary gene name and their amino acid sequence (as extracted from the 'SEQRES' section in their corresponding PDB files). I'm looking for the genomic ...
1
vote
1answer
33 views

Installing Rostlab's PredictProtein

I am trying to install Rostlab's PredictProtein in a Virtual Machine as detailed here https://rostlab.org/owiki/index.php/How_to_Run_The_PredictProtein_Machine_Image_with_VirtualBox: Download ...
3
votes
1answer
57 views

Searching for protein motifs with MEME

I am trying to look for motifs in a set of proteins returned by a mass spec experiment using MEME. The experiment was carried out in the yeast Candida albicans. Does anyone know if it is worth ...
-2
votes
2answers
129 views

Web scraping in R

I have ~130 gene names of different human proteins. I'm looking for a convenient and systematic way to locate each gene's location in the genome, extract its CDS sequence and find whether there are ...
1
vote
1answer
155 views

Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment

My task is to count the mutations occurred in several proteins after a treatment. The sequences are all present in the two files in the same order. I opened both files with the FASTA parser (...
2
votes
0answers
26 views

Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein. The trajectories are from my Gromacs simulation. Firstly I use ...
0
votes
1answer
83 views

How to find/build the evolutionary history of a protein from its sequence?

I would like to build the evolutionary history of a protein. For example given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein for example: ...
3
votes
2answers
75 views

ROC analysis, CAFA 2 experiment

My question is about ROC curves used in CAFA2 experiment. In this paper they used the ROC analysis for the term-centric evaluation. In order to perform ROC curve analysis we should have a continuous ...
1
vote
0answers
10 views

“No records to view” error in the “Drug and Drug Target Mapping” PDB's search engine

I'm using the "Drug and Drug Target Mapping" search engine (http://www.rcsb.org/pdb/ligand/drugMapping.do). I've noticed that there are some drugs (generic names) that if they appear in the query, the ...
4
votes
2answers
100 views

Cross-reference with PDB database

I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those ...
1
vote
0answers
52 views

Map domain names from UniProt bed files to domain accessions

I want to get a bed file mapping human protein domains to the human genome. UniProt actually offers such a thing here. The problem, however, is that the file doesn't include any kind of domain ...
2
votes
0answers
17 views

Folded Protein Chunk Dimensional Classification?

Are there known scales and precisions required of dimensions for the classification of folded proteins given a starting chunk as defined by something like the clustering functionality of MSM Builder? ...
1
vote
1answer
30 views

Proteins that cannot form biofilm?

I am trying to build a machine learning training set for bacterial protein sequences that form biofilm, and that cannot. I collected the positive sequences from the GO ontology website but for ...
5
votes
2answers
71 views

How to determine a protein's cellular location based on its sequence?

I am wondering about the appropriate workflow to determine a protein's cellular location based on its sequence. Let's say I have a sequence like this from a fasta file ...
6
votes
1answer
135 views

Verify a predicted protein in one genome in a different genome of the same species

I have two genome assemblies of the same non-model species, call them Assembly 1 (generated from Illumina data) and Assembly 2 (generated from PacBio data). For Assembly 1, I also have predicted ...
5
votes
1answer
25 views

How to query a network for a bacterium, specifically Streptomyces caatingaensis or Streptomyces thioluteus?

I have a list of gene/protein IDs and I could not query a network using String, BioGrid, Intact and IIS, for Streptomyces thioluteus. The bacteria I am working with is the Streptomyces caatingaensis. ...
1
vote
1answer
191 views

Filtering out all seqs with mutations of list2 from list1

I have 2 lists, list1 and list2, of protein sequences of the same given gene in different strains. In ...
5
votes
3answers
188 views

How to determine the primary Uniprot accession number from a set of accession numbers?

Given a list of Uniprot IDs that are linked to an Ensembl gene ID, is there a way to systematically determine the UniProt accession corresponding to the protein product of the gene's primary ...
4
votes
1answer
23 views

Identity plus Similarity Interpretation

I am helping a colleague to interpret protein multiple sequence alignment results. My colleague used a third-party proprietary solution (I know...) to calculate the alignment, and one of the resulting ...
4
votes
1answer
63 views

Using signal peptide and the expression levels of signal recognition particle in secretome analysis

I have not found any work which investigates assessment of differences in levels of secreted proteins by taking advantage of differential expression of the genes which mediate the secretory pathway. ...
2
votes
2answers
94 views

Why are some of the gene peptides returned by biomaRt missing an asterisk in the end?

Note: this question has also been asked on BioStars I am getting peptides using biomaRt library in R for the gene 'BRCA1'. 27 different aminoacid sequences are returned, and 12 of those have an ...
4
votes
2answers
45 views

Do any publicly available databases detail protein structure and functional domains?

I am interested in finding a database that takes a gene or protein name as input (possibly with the option to specify transcript) and gives information about the protein's functional domains in terms ...
2
votes
2answers
93 views

Influence of pH on protein peptide mass

I'm using the Peptides package in R to calculate the mass of peptides with the mw() method. The thing is that I want to calculate them for different pH values, and thus I wrote this little function to ...
2
votes
1answer
73 views

Building network for biomarker interaction analysis

I am looking for advice on how to best approach a problem I am faced with. I have a dataset of numerous degradative biomarkers, clinical information and various other measures (from clinical trials)....
3
votes
1answer
35 views

Software to produce a table of post-translational modifications from a peptide list

Does anyone know if there is a program/library/script in R or Python that takes as input a list of proteins/peptides and a list of post-translational modifications (PTMs; like oxidation of methionine ...
4
votes
3answers
90 views

Calculating the charge of a peptide computationally

I was wondering how I can calculate the charge of a protein peptide (e.g. "RKTTLVPNTQTASPR") computationally in R or another tool.
5
votes
0answers
32 views

Minimizing Grid Mapping time of Protein Surface

This is an interesting problem - I was wondering if anyone has a creative solution. So I have a vector of vertices representing atoms in a protein, as well as 6 variables containing the absolute ...
5
votes
1answer
59 views

How can I dock a protein to a nucleic acid?

I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules. What tool can I use?