Protein folding simulation with genetic algorithm and supersecondary structure constraints

Yan Cui, Run Sheng Chen, Wing Hung Wong

Research output: Contribution to journalArticle

57 Citations (Scopus)

Abstract

We describe an algorithm to compute native structures of proteins from their primary sequences. The novel aspects of this method are: 1) The hydrophobic potential was set to be proportional to the nonpolar solvent accessible surface. To make computation feasible, we developed a new algorithm to compute the solvent accessible surface areas rapidly. 2) The supersecondary structures of each protein were predicted and used as restraints during the conformation searching processes. This algorithm was applied to five proteins. The overall fold of these proteins can be computed from their sequences, with deviations from crystal structures of 1.48-4.48 Å for C(α) atoms.

Original languageEnglish (US)
Pages (from-to)247-257
Number of pages11
JournalProteins: Structure, Function and Genetics
Volume31
Issue number3
DOIs
StatePublished - May 15 1998
Externally publishedYes

Fingerprint

Protein folding
Protein Folding
Genetic algorithms
Amino Acid Motifs
Proteins
Amino Acid Sequence
Conformations
Crystal structure
Atoms

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Cite this

Protein folding simulation with genetic algorithm and supersecondary structure constraints. / Cui, Yan; Chen, Run Sheng; Wong, Wing Hung.

In: Proteins: Structure, Function and Genetics, Vol. 31, No. 3, 15.05.1998, p. 247-257.

Research output: Contribution to journalArticle

@article{84ce7a81d9f8473f9dbe16982971edda,
title = "Protein folding simulation with genetic algorithm and supersecondary structure constraints",
abstract = "We describe an algorithm to compute native structures of proteins from their primary sequences. The novel aspects of this method are: 1) The hydrophobic potential was set to be proportional to the nonpolar solvent accessible surface. To make computation feasible, we developed a new algorithm to compute the solvent accessible surface areas rapidly. 2) The supersecondary structures of each protein were predicted and used as restraints during the conformation searching processes. This algorithm was applied to five proteins. The overall fold of these proteins can be computed from their sequences, with deviations from crystal structures of 1.48-4.48 {\AA} for C(α) atoms.",
author = "Yan Cui and Chen, {Run Sheng} and Wong, {Wing Hung}",
year = "1998",
month = "5",
day = "15",
doi = "10.1002/(SICI)1097-0134(19980515)31:3<247::AID-PROT2>3.0.CO;2-G",
language = "English (US)",
volume = "31",
pages = "247--257",
journal = "Proteins: Structure, Function and Genetics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "3",

}

TY - JOUR

T1 - Protein folding simulation with genetic algorithm and supersecondary structure constraints

AU - Cui, Yan

AU - Chen, Run Sheng

AU - Wong, Wing Hung

PY - 1998/5/15

Y1 - 1998/5/15

N2 - We describe an algorithm to compute native structures of proteins from their primary sequences. The novel aspects of this method are: 1) The hydrophobic potential was set to be proportional to the nonpolar solvent accessible surface. To make computation feasible, we developed a new algorithm to compute the solvent accessible surface areas rapidly. 2) The supersecondary structures of each protein were predicted and used as restraints during the conformation searching processes. This algorithm was applied to five proteins. The overall fold of these proteins can be computed from their sequences, with deviations from crystal structures of 1.48-4.48 Å for C(α) atoms.

AB - We describe an algorithm to compute native structures of proteins from their primary sequences. The novel aspects of this method are: 1) The hydrophobic potential was set to be proportional to the nonpolar solvent accessible surface. To make computation feasible, we developed a new algorithm to compute the solvent accessible surface areas rapidly. 2) The supersecondary structures of each protein were predicted and used as restraints during the conformation searching processes. This algorithm was applied to five proteins. The overall fold of these proteins can be computed from their sequences, with deviations from crystal structures of 1.48-4.48 Å for C(α) atoms.

UR - http://www.scopus.com/inward/record.url?scp=0009636533&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0009636533&partnerID=8YFLogxK

U2 - 10.1002/(SICI)1097-0134(19980515)31:3<247::AID-PROT2>3.0.CO;2-G

DO - 10.1002/(SICI)1097-0134(19980515)31:3<247::AID-PROT2>3.0.CO;2-G

M3 - Article

VL - 31

SP - 247

EP - 257

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

SN - 0887-3585

IS - 3

ER -