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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12 votes
1 answer
113 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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10 votes
4 answers
774 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....
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8 votes
2 answers
814 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 ...
  • 313
7 votes
0 answers
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 ...
6 votes
3 answers
85 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 ...
  • 63
6 votes
2 answers
219 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 ...
  • 743
6 votes
2 answers
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 ...
  • 1,022
6 votes
3 answers
640 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.
  • 575
6 votes
1 answer
156 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 ...
  • 2,656
6 votes
1 answer
69 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. ...
5 votes
3 answers
3k views

How to translate amino acid sequences to Nucleotide sequences

I want to convert a list of fasta ( protein sequences) in a .text file into corresponding nucleotide sequences. A Google search gives me result of DNA to protein conversion but not vice versa. Also, I ...
5 votes
3 answers
566 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 ...
5 votes
1 answer
101 views

BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure

I am using the internal_coords module from BioPython in order to compare dihedral angles of two different conformations of the same protein. The conformations are ...
  • 405
5 votes
2 answers
87 views

Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles

I have been successfully using BioPython's functionality for extracting protein torsion angles using the IC_Chain module. However, I am currently looking to use the ...
  • 405
5 votes
1 answer
147 views

Identify side chain atoms in BioPandas dataframe

I am currently implementing some metrics I could use for comparing two conformations of the same protein in Python. For example, I know I could use the RMSD of all protein ATOMS in BioPandas using ...
  • 405
5 votes
1 answer
92 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?
5 votes
1 answer
43 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. ...
  • 161
5 votes
0 answers
238 views

What exactly does each of InterPro, PANTHER, Pfam bring to the table individually in classifying a protein?

I would be very grateful if somebody could sketch out the methods Pfam and PANTHER use to assign a family to a given protein and how they are different. My (cursory) understanding is that InterpProp ...
  • 270
5 votes
0 answers
243 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 ...
  • 8,225
4 votes
4 answers
167 views

Database for proteome-wide predictions of protein structures

Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I ...
4 votes
2 answers
34k 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 ...
  • 85
4 votes
2 answers
414 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 ...
4 votes
4 answers
149 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: ...
  • 1,407
4 votes
1 answer
516 views

How could I match atom orders between a .mol2 and a .pdb?

When I was drawing conformation of Autodock result, I noticed that Autodock generated pdbqt from dlg has some structural problem (e.g. Benzene ring missing), and wants to correct this. However I ...
4 votes
1 answer
61 views

On the same strand, for the same gene, can exons be overlapping?

I want to get a set of exon regions for each protein coding gene. I extracted a set of relevant information (chromosome, start, end, gene ID, gene name, gene type, exon number and exon ID) from a GTF ...
  • 1,733
4 votes
1 answer
185 views

How do I get GO annotations for a list of UniProt IDs?

I have a list of UniProt ids that I want to get Gene Ontology annotations for. I need this information because I want this high-level information as an input to a neural network. The model I wish to ...
  • 43
4 votes
1 answer
368 views

CCP4 file to a Python 3 numpy array or similar workaround

I would like to merge together several ccp4 formatted density maps (and do a few minor things). So ideally I would like to open the ccp4/mrc files as numpy arrays in Python 3 and save the array as a ...
  • 3,854
4 votes
1 answer
117 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 ...
4 votes
2 answers
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 ...
  • 91
4 votes
2 answers
157 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 votes
1 answer
42 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
1 answer
131 views

Programmatic way of accessing the FASTA sequence similarity tool (or similar) in Python

I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command ...
  • 405
4 votes
1 answer
64 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 ...
  • 575
4 votes
1 answer
89 views

Is there a modern alignment tool tailored for transmembrane regions?

I am looking for a project or tool that allows programmatic pairwise alignments of proteins but that takes care with transmembrane regions of proteins. TM regions are traditionally too information ...
  • 399
4 votes
1 answer
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. ...
  • 524
3 votes
2 answers
228 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 ...
  • 295
3 votes
2 answers
361 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 ...
  • 575
3 votes
1 answer
131 views

What is the origin of HIV1?

What is the origin of HIV1? This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1 ...
  • 215
3 votes
2 answers
198 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: ...
  • 1,407
3 votes
1 answer
30 views

How can I parse alternative atom information?

I am trying to parse PDB files. Say, a PDB file has the following data: ...
3 votes
1 answer
37 views

What is the function of the heteroatoms

I am trying to make a prediction application using the sequence of proteins. If we think about the 6COU protein, I'm running the code below ...
  • 133
3 votes
1 answer
38 views

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

I have a dataset about adundance of urine proteins from cancer patients. I would like to compare these abundance levels to healthy patients' urine proteins. However I don't have any data with healthy ...
3 votes
1 answer
75 views

How to filter the PDB for single-domain proteins with full length 3D-structures solved

I am trying to reproduce a machine learning model that has been developed here. As one of the datasets, they use single-domain proteins with full length 3D-structures solved. Since I don't have a ...
3 votes
1 answer
77 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 ...
3 votes
3 answers
122 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. ...
3 votes
2 answers
165 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 ...
  • 151
3 votes
1 answer
91 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 ...
3 votes
1 answer
43 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 ...
  • 195
3 votes
1 answer
195 views

Perform protein structure-based sequence alignment in Python

I am looking for a Python package that performs pairwise structural alignment of protein structures (i.e., PDB files) and returns a sequence alignment. PyMOL is able to do this through the GUI, for ...
3 votes
1 answer
274 views

How do you calculate the top L/5 score?

I am currently investigating how to predict protein structure and contact map predictions. There, I see things like top L/5 and top L/2 scores as a way to evaluate the contact map. What formulas do ...