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.

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3
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1answer
78 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 ...
2
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1answer
136 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
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1answer
46 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
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2answers
285 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
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1answer
139 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
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2answers
266 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....
4
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1answer
108 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
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1answer
44 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 ...
2
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1answer
150 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 ...
-1
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2answers
275 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
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1answer
439 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 (...
3
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0answers
83 views

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

I am using VMD to visualise the secondary structure of protein here. The trajectories are from my Gromacs simulation. Firstly I use ...
3
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2answers
169 views

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

I'd like to build the evolutionary history of a protein, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein as an example: ...
4
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2answers
84 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
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0answers
12 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
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2answers
137 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 ...
4
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0answers
210 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 ...
3
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1answer
41 views

Folded Protein Chunk Dimensional Classification?

Are there known dimensional measurements for the classification of folded proteins given a starting chunk/domain as defined by something like the clustering functionality of MSM Builder? Examples of ...
2
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1answer
48 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 ...
6
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2answers
119 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
151 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
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1answer
38 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
232 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
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3answers
484 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
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1answer
38 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
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1answer
71 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. ...
3
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2answers
194 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 ...
6
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3answers
72 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 ...
3
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2answers
296 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 ...
3
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1answer
114 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)....
4
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1answer
59 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 ...
6
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3answers
495 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.
7
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0answers
69 views

Minimizing particle-flow grid mapping time of a protein surface using spherical-coordinates and differentiation encoding [closed]

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
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1answer
73 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?
6
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2answers
1k views

How to select a cutoff for interaction confidence in STRINGdb?

I have a list of 100 genes that are called as hits in a genetic screening. I want to have a network of the interactions between the proteins of these 100 genes. I am using both STRINGdb web and its R ...
4
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4answers
138 views

What are the standard ways to visualize protein-protein or gene-gene interactions?

I would like to visualize this interaction list. Is there an online/web based way to do it? Is there a way to analyze the data? Assuming I have exported the list into lines such as: ...
6
votes
1answer
58 views

How do I compare measured ratios to calculated ratios in peptide mass spectrometry?

I have two different sets of internal standards in a sample (1), and a sample (2) with these internal standards as well as about 30 peptides. Each peptide has one of each of these kind of standards. ...
10
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4answers
737 views

How can I build a protein network pathway from a gene expression quantification file?

Assume I have found the top 0.01% most frequent genes from a gene expression file. Let's say, these are 10 genes and I want to study the protein protein interactions, the protein network and pathway....
2
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2answers
817 views

Protein folding problem model for quantum computers?

It's supposed that quantum computers could help to find the native state of all human DNA proteins. Does anyone know how to formulate the protein folding problem into a decision problem solvable ...
8
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2answers
686 views

Phyre2 vs ITasser, completely different models generated

Does anyone have experience generating pdb structures with Phyre and ITasser online tools. The results generated from each given the same amino acid sequence input are very different and I am ...
11
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1answer
104 views

What are the optimal parameters for docking a large ligand using Hex?

I'm looking to dock a large ligand (~90kDa) to a receptor slightly larger receptor (~125kDa) using Hex. If anyone is familiar with docking large structures, are there any recommended parameters for ...

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