A new branch and bound method for the protein folding problem under the 2D-HP model

Sun Yuan Hsieh, De Wei Lai

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

Abstract

The protein folding problem is a fundamental problem in computational molecular biology and biochemical physics. The previously best known branch and bound method for the protein folding problem may find optimal or near-optimal energy structure from the benchmark sequences, but the total computation time is rather lengthy because it usually needs to run a great deal of simulating tests or else lack of accuracy. In this paper, we develop a new branch and bound method for the the protein folding problem under the two-dimensional HP model to overcome the mentioned drawbacks. By using benchmark sequences for evaluation, we demonstrate that the performance of our method is superior than previously known methods. Moreover, our method is a simple, flexible and easily implemented one for the protein folding problem.

Original languageEnglish
Article number5942173
Pages (from-to)69-75
Number of pages7
JournalIEEE Transactions on Nanobioscience
Volume10
Issue number2
DOIs
Publication statusPublished - 2011 Jun 1

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Medicine (miscellaneous)
  • Biomedical Engineering
  • Pharmaceutical Science
  • Computer Science Applications
  • Electrical and Electronic Engineering

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