The program FANTOM for energy refinement of polypeptides and proteins using a Newton – Raphson minimizer in torsion angle space

Thomas Schaumann, Werner Braun, Kurt Wüthrich

Research output: Contribution to journalArticle

91 Scopus citations

Abstract

The program FANTOM (fast Newton–Raphson torsion angle energy minimizer) performs minimizations of the ECEPP/2 energy function for proteins with the Newton–Raphson method. It is implemented for use with conventional computer hardware. The torsion angles are chosen as independent variables. The first and second derivatives are calculated with a previously described rapid algorithm. For the matrix inversion a modified Cholesky factorization is used. A line search adjusts the step length and nonbonded interactions can be calculated with a cutoff. The following tests of the program are described: All local minima of the ECEPP/2 energy function for the amino acids glycine and alanine were determined. An exhaustive search by more than 16,000 independent energy minimizations was used to identify low‐energy structures of Met‐enkephalin, which were then compared with previously published structures of this pentapeptide. To investigate the use of FANTOM with disulfide bonds, it was applied with conotoxin. As an illustration of the intended primary use of the program, an energy refinement of the structure of the basic pancreatic trypsin inhibitor determined by nmr spectroscopy in solution is described.

Original languageEnglish (US)
Pages (from-to)679-694
Number of pages16
JournalBiopolymers
Volume29
Issue number4-5
DOIs
StatePublished - Jan 1 1990
Externally publishedYes

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Biomaterials
  • Organic Chemistry

Fingerprint Dive into the research topics of 'The program FANTOM for energy refinement of polypeptides and proteins using a Newton – Raphson minimizer in torsion angle space'. Together they form a unique fingerprint.

  • Cite this