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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5
votes
3answers
1k 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 ...
3
votes
2answers
162 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: ...
10
votes
4answers
725 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
votes
2answers
596 views

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 ...
1
vote
1answer
56 views

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 ...
3
votes
3answers
93 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. ...
0
votes
1answer
792 views

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/...