@inbook{d13120af31164ae9ad67bf097ee5b1da,

title = "Stochastic protein folding simulation in the D-dimensional HP-Model",

abstract = "We present results from two- and three-dimensional protein folding simulations in the HP-model on selected benchmark problems. The importance of the HP-model for investigating general complexity issues of protein folding has been recently demonstrated by Fu & Wang (LNCS 3142:630-644, 2004) in proving an exp(O(n(1-1/d) . ln n)) time bound for d-dimensional protein folding simulation of sequences of length n. The time bound is close to the approximation of real folding times of exp(lambda . n(2/3) +/- chi . n(1/2)/2)ns by Finkelstein & Badretdinov (FOLD DES 2:115-121, 1997), where lambda and chi are constants close to unity. We utilise a stochastic local search procedure that is based on logarithmic simulated annealing. We obtain that after (m/delta)(a.D) Markov chain transitions the probability to be in a minimum energy conformation is at least 1 - delta, where m ",

author = "K Steinhofel and A Skaliotis and Albrecht, {A A} and S Hochreiter and R Wagner",

year = "2007",

language = "English",

isbn = "0302-9743",

volume = "4414 LNBI",

series = "LECTURE NOTES IN COMPUTER SCIENCE",

publisher = "Springer",

pages = "381 -- 394",

booktitle = "Bioinformatics Research and Development, Proceedings",

note = "1st International Conference on Bioinformatics Research and Development ; Conference date: 01-01-2007",

}