The Ultimate Speed Limit to Protein Folding Is Conformational Searching

2007 ◽  
Vol 129 (39) ◽  
pp. 11920-11927 ◽  
Author(s):  
Kingshuk Ghosh ◽  
S. Banu Ozkan ◽  
Ken A. Dill
Keyword(s):  
Protein Folding ◽  
Speed Limit ◽  
Conformational Searching

scholarly journals Speed limit of protein folding evidenced in secondary structure dynamics

2011 ◽  
Vol 108 (40) ◽  
pp. 16622-16627 ◽  
Author(s):  
M. M. Lin ◽  
O. F. Mohammed ◽  
G. S. Jas ◽  
A. H. Zewail
Keyword(s):  
Protein Folding ◽  
Secondary Structure ◽  
Speed Limit ◽  
Structure Dynamics

scholarly journals The speed limit for protein folding measured by triplet-triplet energy transfer

1999 ◽  
Vol 96 (17) ◽  
pp. 9597-9601 ◽  
Author(s):  
O. Bieri ◽  
J. Wirz ◽  
B. Hellrung ◽  
M. Schutkowski ◽  
M. Drewello ◽  
...  
Keyword(s):  
Protein Folding ◽  
Energy Transfer ◽  
Speed Limit ◽  
Triplet Energy ◽  
Triplet Energy Transfer

scholarly journals A speed limit for protein folding.

1996 ◽  
Vol 93 (21) ◽  
pp. 11426-11427 ◽  
Author(s):  
J. A. McCammon
Keyword(s):  
Protein Folding ◽  
Speed Limit

Reaching the protein folding speed limit with large, sub-microsecond pressure jumps

2009 ◽  
Vol 6 (7) ◽  
pp. 515-519 ◽  
Author(s):  
Charles Dumont ◽  
Tryggvi Emilsson ◽  
Martin Gruebele
Keyword(s):  
Protein Folding ◽  
Speed Limit

BÉZIER SUBDIVISION FOR INVERSE MOLECULAR KINEMATICS

2006 ◽  
Vol 16 (05n06) ◽  
pp. 513-532 ◽  
Author(s):  
MING ZHANG ◽  
LIQUN WANG ◽  
RONALD GOLDMAN
Keyword(s):  
Protein Folding ◽  
Protein Structure ◽  
Ab Initio ◽  
Polynomial Equations ◽  
Profound Impact ◽  
Conformational Searching ◽  
Ab Initio Prediction ◽  
Specific Geometry

Conformational searching is a core task in inverse molecular kinematics. Algorithmic improvements affecting either the speed or quality of conformational searching will have a profound impact on applications including ligand-receptor docking, ab initio prediction of protein structure, and protein folding. In this paper, we investigate a specific geometry-constrained conformational searching problem, where some feature atoms have pre-specified target positions. Using Bézier subdivision, we present a method to locate and approximate the solutions of the equations derived from constraints on the feature atoms. The conformations corresponding to these solutions are all the conformations satisfying the target constraints. Three implementations of the subdivision method taking advantage of the sparsity of the coefficients of the polynomial equations are presented and the results are compared and contrasted.

scholarly journals The protein folding ‘speed limit’

2004 ◽  
Vol 14 (1) ◽  
pp. 76-88 ◽  
Author(s):  
Jan Kubelka ◽  
James Hofrichter ◽  
William A Eaton
Keyword(s):  
Protein Folding ◽  
Speed Limit
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