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

T. Schaumann, Werner Braun, K. Wuthrich

Research output: Contribution to journalArticle

90 Citations (Scopus)

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
StatePublished - 1990
Externally publishedYes

Fingerprint

Conotoxins
Methionine Enkephalin
Aprotinin
Polypeptides
Disulfides
Alanine
Torsional stress
Glycine
Spectrum Analysis
Proteins
Amino Acids
Peptides
Amino acids
Newton-Raphson method
Factorization
Computer hardware
Spectroscopy
Derivatives

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

The program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space. / Schaumann, T.; Braun, Werner; Wuthrich, K.

In: Biopolymers, Vol. 29, No. 4-5, 1990, p. 679-694.

Research output: Contribution to journalArticle

@article{39f52eb76c224fc1a708d59b27dcd402,
title = "The program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space",
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.",
author = "T. Schaumann and Werner Braun and K. Wuthrich",
year = "1990",
language = "English (US)",
volume = "29",
pages = "679--694",
journal = "Biopolymers",
issn = "0006-3525",
publisher = "John Wiley and Sons Inc.",
number = "4-5",

}

TY - JOUR

T1 - The program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space

AU - Schaumann, T.

AU - Braun, Werner

AU - Wuthrich, K.

PY - 1990

Y1 - 1990

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=0025344281&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0025344281&partnerID=8YFLogxK

M3 - Article

VL - 29

SP - 679

EP - 694

JO - Biopolymers

JF - Biopolymers

SN - 0006-3525

IS - 4-5

ER -