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Abalone (molecular mechanics)

Protein model on Abalone
DNA model on Abalone

Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit water (Flexible SPC[1]) or in implicit water models.[2] Mainly designed to simulate the proteins folding and DNA-ligand complexes in AMBER force field.

Contents

  • The key features 1
  • See also 2
  • References 3
  • External links 4

The key features

See also

References

  1. ^ Toukan K and Rahman A (1985). "Molecular-dynamics study of atomic motions in water". Physical Review B 31 (5): 2643–2648.  
  2. ^ Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990). "Semianalytical treatment of solvation for molecular mechanics and dynamics". J Am Chem Soc 112 (16): 6127–6129.  
  3. ^ Y. Sugita and Y. Okamoto (1999). "Replica-exchange molecular dynamics method for protein folding". Chemical Physics Letters 314: 141–151.  

External links

  • Home page
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