Predicting solvated peptide conformations via global minimization of energetic atom-to-atom interactions

J. L. Klepeis, I. P. Androulakis, M. G. Ierapetritou, C. A. Floudas

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

A global optimization method is described for identifying the global minimum energy conformation, as well as lower and upper bounds on the global minimum conformer of solvated peptides. Potential energy contributions are calculated using the ECEPP/3 force field model. In considering the effects of hydration, two implicit free energy models are compared. One method is based on the calculation of solvent-accessible surface areas, while the other uses information on the solvent-accessible volume of hydration shells. Detailed information on the potential and solvation energy contributions is presented for the terminally blocked single residue peptides. In addition, based on a procedure that allows the exclusion of domains of the (φ, ψ) space, a number of oligopeptide structure prediction problems are considered, and the role of the solvation model in defining global minimum conformations is addressed.

Original languageEnglish (US)
Pages (from-to)765-788
Number of pages24
JournalComputers and Chemical Engineering
Volume22
Issue number6
DOIs
StatePublished - Jun 20 1998
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Chemical Engineering(all)
  • Computer Science Applications

Keywords

  • Global optimization
  • Protein folding
  • Solvation

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