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Protocol publication

[…] The interactions of PAP248-286 with the molecular tweezer CLR01 and the spacer CLR03 were investigated using Replica Exchange Molecular Dynamics (REMD) simulations (; ) performed with Gromacs 4.6 () and the CHARMM27 force field (; ). The water solvent was treated explicitly using the TIP3P model (). The parameters for CLR01 and CLR03 were obtained using the Swissparam server and tested previously (; ). The initial coordinates of PAP248-286 were taken from the Protein Data Bank, code 2L3H (). The temperature range for the REMD simulations was 290–330 K. The temperature distribution was obtained as described by . Here, we focused our discussion on the 300 K trajectory. Three systems were investigated: (1) PAP248-286, (2) PAP248-286 with 7 CLR01 molecules (one for each Lys or Arg residue, with the exception of Lys272 which was not sterically accessible in the initial structure but became available during the simulations), and (3) PAP248-286 with 8 CLR03 molecules interacting via the hydrogen phosphate groups with each Lys or Arg residue of PAP248-286. For each system, 22 replicas were simulated during 60 ns. The cluster analysis of the REMD simulations was performed with the gromos method using a cut-off value of 0.2 nm (). […]

Pipeline specifications

Software tools GROMACS, SwissParam
Application Drug design
Organisms Human immunodeficiency virus 2
Diseases Virus Diseases, HIV Infections, Amyloid Neuropathies