Computational protocol: Energetics of side-chain partitioning of β-signal residues in unassisted folding of a transmembrane β-barrel protein

Similar protocols

Protocol publication

[…] All molecular dynamics simulations were performed at a constant temperature of 310 K and a constant pressure of 1 bar, using GROMACS version 5.0.4 (), using previously reported protocols (). Using the CHARMM-GUI () input generator, we embedded the protein molecule (PagP crystal structure, PDB code 1THQ ()) in a micelle system consisting of 80 DPC molecules. We first equilibrated the protein–micelle complex and followed it up with a production molecular dynamics simulation of 10 ns. Vicinity analysis was performed using VMD (Visual Molecular Dynamics) (). […]

Pipeline specifications

Software tools GROMACS, CHARMM, VMD
Application Protein structure analysis
Chemicals Amino Acids