Helix folding of an alanine-based peptide in explicit water
Article Abstract:
The folding of a 16-residue alanine-based helical peptide in explicit water is studied using computer simulations that employ full atomic representations for both the peptide and water molecules, self-guided molecular dynamics method and molecular dynamics (MD) simulations. The analysis of the simulation trajectories exhibited that the multiple major conformational clusters with one or more helix segments in the peptide is adopted by the alanine-based peptide.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2001
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Conformation changes, complexation, and phase transition in matrix-assisted laser desorption
Article Abstract:
Molecular dynamics simulations were applied for displaying that the guest species in matrix-assisted laser desorption exhibit significantly different conformations in the gas phase, on the crystal surface and embedded into the matrix. Results indicated that the maximum energy transfer occurred during the phase transition of the host crystal at which time the guest species were released from the crystal.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2001
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Folding studies of a linear pentamer peptide adopting a reverse turn conformation aqueous solution through molecular dynamics simulation
Article Abstract:
A cluster analysis method was developed based on conformational population and used to analyze the trajectories of the 2 ns self-guided molecular dynamics (SGMD) simulation. Five major conformational clusters were obtained from the 2 ns SGMD simulation and the most populated conformational cluster is a type II reverse turn-like conformation.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2000
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