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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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(Complete) Stuctural Models of Antibodies: Combining Fc and Fab from pdb to Build Hinge Region? Or what?

I'm a newcomer to the field of antibodies, and I'm seeking guidance on obtaining 3D structures for my molecular simulations. After browsing the PDB databank, I noticed that there are Fab and Fc ...
LameSloth's user avatar
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
1 vote
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Energy error margin for protein structures

I would like to know the acceptable error margin for the lowest free energy of a protein. In other words, say, both Group A and B have determined the lowest free energy of the same protein in their ...
Omar Shehab's user avatar
1 vote
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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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1 vote
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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