Protein folding using fragment assembly and physical energy function

Seung Yeon Kim, Weontae Lee, Julian Lee

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)


We perform a systematic study of the effects of sequence-independent backbone interactions and sequence-dependent side-chain interactions on protein folding using fragment assembly and physical energy function. Structures for ten proteins belonging to various structural classes are predicted only with Lennard-Jones interaction between backbone atoms. We find nativelike structures for Β proteins, suggesting that for proteins in this class, the global tertiary structures can be determined mainly by sequence-independent backbone interactions. On the other hand, for α proteins, nonlocal hydrophobic side-chain interaction is also required to obtain nativelike structures.

Original languageEnglish
Article number194908
JournalJournal of Chemical Physics
Issue number19
Publication statusPublished - 2006

Bibliographical note

Funding Information:
This work was supported by the NRL program of MOST NRDP (M1–0203–00–0020). The authors thank Kyoungrim Lee for useful discussions.

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry


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