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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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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, ...
Amal Brikci-Nigassa's user avatar
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 ...
sin tribu's user avatar
  • 221
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 ...
James's user avatar
  • 409
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 ...
James's user avatar
  • 409