Molecular Dynamics with the United-Residue Model of Polypeptide Chains. II. Langevin and Berendsen-Bath Dynamics and Tests on Model α-Helical Systems

This publication has 59 references indexed in Scilit:

• Molecular Dynamics with the United-Residue Model of Polypeptide Chains. I. Lagrange Equations of Motion and Tests of Numerical Stability in the Microcanonical Mode
  The Journal of Physical Chemistry B, 2005
• Energy‐based reconstruction of a protein backbone from its α‐carbon trace by a Monte‐Carlo method
  Journal of Computational Chemistry, 2002
• A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization
  Journal of Computational Chemistry, 1997
• AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
  Computer Physics Communications, 1995
• Prediction of protein conformation on the basis of a search for compact structures: Test on avian pancreatic polypeptide
  Protein Science, 1993
• On the Approximation of Solvent Effects on the Conformation and Dynamics of Cyclosporin A by Stochastic Dynamics Simulation Techniques
  Molecular Simulation, 1988
• A Leap-frog Algorithm for Stochastic Dynamics
  Molecular Simulation, 1988
• Molecular dynamics with coupling to an external bath
  The Journal of Chemical Physics, 1984
• Comparison of simple potential functions for simulating liquid water
  The Journal of Chemical Physics, 1983
• A simplified representation of protein conformations for rapid simulation of protein folding
  Journal of Molecular Biology, 1976