Stochastic protein folding simulation in the D-dimensional HP-Model

K Steinhofel, A Skaliotis, A A Albrecht, S Hochreiter (Editor), R Wagner (Editor)

Research output: Chapter in Book/Report/Conference proceedingConference paper

9 Citations (Scopus)


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
Original languageEnglish
Title of host publicationBioinformatics Research and Development, Proceedings
Place of PublicationBERLIN
Pages381 - 394
Number of pages14
Volume4414 LNBI
ISBN (Print)0302-9743
Publication statusPublished - 2007
Event1st International Conference on Bioinformatics Research and Development - Berlin, Germany
Duration: 1 Jan 2007 → …

Publication series



Conference1st International Conference on Bioinformatics Research and Development
Period1/01/2007 → …


Dive into the research topics of 'Stochastic protein folding simulation in the D-dimensional HP-Model'. Together they form a unique fingerprint.

Cite this