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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Processing proteomics data
[this question was also asked on BioStars]
In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes marked ...
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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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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 ...
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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 ...
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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 ...
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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 ...
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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.
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Setting up MaxQuant parameters for processing proteomics data
This is a follow up to my previous question here.
In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes ...
- 125
3
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2
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missed cleavages combinations generation
I am looking for an R based solution to the following problem:
Trypsin does not cleave perfectly in proteomics experiments. So starting from a protein sequence FASTA I want to generate all possible ...
3
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2
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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:
...
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What value of reference RMSD after docking simulation from any starting coordinate would be considered outrageous to have?
I need to lightly verify a set of docking simulations from the reference RMSD of the outputs, and as we all know reference RMSD depends on the initial coordinates of the ligand set. What value of ...
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Heat map of protein expression from normalized abundance
This is a follow up to my question posted here
Processing proteomics data
In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article ...
- 125
1
vote
0
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How can I compute energy from a protein PDB file?
Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in the file.
How can I do that?
Sometimes people suggest using the ...
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How to allow "half windows" in biopython?
I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window ...
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Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions
I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this?
Input: a list of unaligned ...
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1
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How to calculate RMSD and binding energy from the already docked ligand-receptor
I have the following PDB file that looks like this.
It is downloadable here. This PDB already contains ligand and receptor together.
The red molecule is the ligand and the yellow is the receptor.
They'...
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How to interpret the GROMACS MD Simulation RMSD Graph?
Hello brilliant researchers!
After virtual screening, I performed MD Simulation via GROMACS to check the stability of the protein-top hit complex by following this tutorial http://www.mdtutorials.com/...
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