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Questions tagged [membrane-protein]

A protein comprising at least one hybdrophobic domain which attaches/anchors within the lipid bilayer of an animal cell. A chanel protein is a special case of a membrane protein.

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2 votes
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Determination of transmembrane domain limits using multiple prediction tools

Integral membrane proteins are proteins that have at least one transmembrane (TM) segment. I performed predictions of TM domains using three tools: ProtScale, ΔG predictor 1.0, TOPCONS. For example, ...
4 votes
1 answer

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 ...
3 votes
1 answer

Gromacs molecular dynamic simulation throwing error during minimization

I am trying to investigate a membrane proteins influence on a lipid bilayer using molecular dynamics. I am new to MD and trying to run my first simulation. I have built the simulation input files ...
5 votes
0 answers

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 ...