Article (Scientific journals)
Limited conformational space for early-stage protein folding simulation
Brylinski, M.; Jurkowski, Wiktor; Konieczny, L. et al.
2004In Bioinformatics, 20 (2), p. 199-205
Peer reviewed
 

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Abstract :
[en] MOTIVATION: The problem of early-stage protein folding is critical for protein structure prediction. The model presented introduces a common definition of protein structures which may be treated as the possible in silico early-stage form of the polypeptide chain. Limitation of the conformational space to the ellipse path on the Ramachandran map was tested as a possible sub-space to represent the early-stage structure for simulation of protein folding. The proposed conformational sub-space was developed on the basis of the backbone conformation, with side-chain interactions excluded. RESULTS: The ellipse-path-limited conformation of BPTI was created using the criterion of shortest distance between Phi, Psi angles in native form of protein and the Phi, Psi angles belonging to the ellipse. No knots were observed in the structure created according to ellipse-path conformational sub-space. The energy minimization procedure applied to ellipse-path derived conformation directed structural changes toward the native form of the protein with SS-bonds system introduced to the procedure. AVAILABILITY: Program 'Ellipse' to create the ellipse-path derived structure available on request: myroterm@cyf-kr.edu.pl
Disciplines :
Biochemistry, biophysics & molecular biology
Identifiers :
UNILU:UL-ARTICLE-2012-589
Author, co-author :
Brylinski, M.
Jurkowski, Wiktor ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Konieczny, L.
Roterman, I.
External co-authors :
yes
Language :
English
Title :
Limited conformational space for early-stage protein folding simulation
Publication date :
2004
Journal title :
Bioinformatics
ISSN :
1367-4803
eISSN :
1460-2059
Publisher :
Oxford University Press - Journals Department, Oxford, United Kingdom
Volume :
20
Issue :
2
Pages :
199-205
Peer reviewed :
Peer reviewed
Available on ORBilu :
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