Questions tagged [structural-biology]

Questions relating to the structure (3-D conformation) of biological molecules, such as protein, RNA and DNA.

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What is a sensible forcefield choice for membrane proteins when using PDB2PQR?

I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. The goal is to calculate the electrostatic charge across the surface of the protein. There are no ...
James's user avatar
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2 votes
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Writing to .cif from BioPandas

My question is twofold. First, I've run into an issue working with .cif files and pandas dataframes. With BioPandas, I can read a .pdb file into a dataframe and then go the opposite direction, writing ...
Brookspj's user avatar
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The difference between sequence-independent and sequence-order independent structural alignment?

I am confused about the difference between sequence-independent and sequence-order independent structural alignment. TM-align for example claims to be sequence-independent; however, I've seen it is ...
fcan's user avatar
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How to identify different protein domains using HHpred

I am new to HHpred/ analyzing proteins so bare with me. I have been given an uncharacterized protein, whose FASTA sequence I have obtained from Uniprot. I am looking to do the following by using ...
microbeprincess's user avatar