Proteins Wriggle

Details Proteins Wriggle Proteins Wriggle

2001-08-14

arxiv.org/abs/cond-mat/0108218v2

Biophys. J. 82(2002)2665-2670

Physics

Condensed Matter

Soft Condensed Matter

12 pages, 2 figures, JHEP latex

Scientific paper

10.1016/S0006-3495(02)75608-7

We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model when proteins fold under physiological conditions, their backbone dihedral angles change synchronously in groups of four or more so as to avoid steric clashes and respect the kinematic conservation laws. They wriggle; they do not thrash. We describe a simple algorithm that can be used to incorporate wriggling in Monte Carlo simulations of protein folding. We have tested this wriggling algorithm against a code in which the dihedral angles are varied independently (thrashing). Our standard of success is the average root-mean-square distance (rmsd) between the alpha-carbons of the folding protein and those of its native structure. After 100,000 Monte Carlo sweeps, the relative decrease in the mean rmsd, as one switches from thrashing to wriggling, rises from 11% for the protein 3LZM with 164 amino acids (aa) to 40% for the protein 1A1S with 313 aa and 47% for the protein 16PK with 415 aa. These results suggest that wriggling is useful and that its utility increases with the size of the protein. One may implement wriggling on a parallel computer or a computer farm.

Affiliated with

Also associated with

No associations

Rating

Proteins Wriggle does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Proteins Wriggle, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Proteins Wriggle will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-135819