Apr 25, 2020

A peptide bond based energy score improve identification of the native structures

BioRxiv : the Preprint Server for Biology
l. wuxia

Abstract

Protein structure resolution has lagged far behind sequence determination, as it is often laborious and time-consuming to resolve individual protein structure, which is more often than not even impossible. For computational prediction, due to the lack of detailed knowledge on the folding driving forces, how to design an energy function is still an open question. Furthermore, an effective criterion to evaluate the performance of the energy function is also lacking. Here we present a novel knowledge-based-energy scoring function, simply considering the interactions of peptide bonds, rather than, as conventionally, the residues or atoms as the most important energy contribution. This energy scoring was evaluated by selecting the Xray structure from a large number of possibilities. It not only outperforms the best of the previously published statistical potentials, but also has very low computational expense. Besides, we suggest an alternative criterion to evaluate the performance of the energy scoring function, measured by the template modeling score of the selected rank-one. We argue that the comparison should allow for some deviation between the x-ray and predicted structures. Collectively, this accurate and simple energy scorin...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Pathologic Cytolysis
Motival
Fluctuation
Bacterial cell
Cellular Process
Genes
Protoplasm
Environment
Bacteriophages
Dicom Derivation

Related Feeds

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Khem Raj GhusingaAbhyudai Singh
Mathematical Biosciences and Engineering : MBE
Qiuying LiJianshe Yu
PLoS Computational Biology
Shivam GuptaAndrew Mugler
© 2020 Meta ULC. All rights reserved