Simulation of peptide folding with explicit water - A mean solvation method

Xiong Wu Wu, Shen Shu Sung

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


A new approach to efficiently calculate solvent effect in computer simulation of macromolecular systems has been developed. Explicit solvent molecules are included in the simulation to provide a mean solvation force for the solute conformational search. Simulations of an alanine dipeptide in aqueous solution showed that the new approach is significantly more efficient than conventional molecular dynamics method in conformational search, mainly because the mean solvation force reduced the solvent damping effect. This approach allows the solute and solvent to be simulated separately with different methods. For the macromolecule, the rigid fragment constraint dynamics method we developed previously allows large time-steps. For the solvent, a combination of a modified force-bias Monte Carlo method and a preferential sampling can efficiently sample the conformational space. A folding simulation of a 16-residue peptide in water showed high efficiency of the new approach.

Original languageEnglish (US)
Pages (from-to)295-302
Number of pages8
JournalProteins: Structure, Function and Genetics
Issue number3
StatePublished - Feb 15 1999

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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