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Osoda T, Miyano S. 2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope. J Cheminform. 2011;3(1):50doi: 10.1186/1758-2946-3-50.
Osoda, T., & Miyano, S. (2011). 2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope. Journal of cheminformatics, 3(1), 50. https://doi.org/10.1186/1758-2946-3-50
Osoda, Tsutomu, and Miyano, Satoru. "2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope." Journal of cheminformatics vol. 3,1 (2011): 50. doi: https://doi.org/10.1186/1758-2946-3-50
Osoda T, Miyano S. 2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope. J Cheminform. 2011 Nov 02;3(1):50. doi: 10.1186/1758-2946-3-50. PMID: 22047717; PMCID: PMC3225324.
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J Cheminform. 2011 Nov 02;3(1):50. doi: 10.1186/1758-2946-3-50.

2D-Qsar for 450 types of amino acid induction peptides with a novel substructure pair descriptor having wider scope.

Journal of cheminformatics

Tsutomu Osoda, Satoru Miyano

Affiliations

  1. Department of Information Science and Technology, The University of Tokyo, Shiroganedai 4-6-1, Minato-ku, Tokyo, Japan. [email protected].

PMID: 22047717 PMCID: PMC3225324 DOI: 10.1186/1758-2946-3-50

Abstract

BACKGROUND: Quantitative structure-activity relationships (QSAR) analysis of peptides is helpful for designing various types of drugs such as kinase inhibitor or antigen. Capturing various properties of peptides is essential for analyzing two-dimensional QSAR. A descriptor of peptides is an important element for capturing properties. The atom pair holographic (APH) code is designed for the description of peptides and it represents peptides as the combination of thirty-six types of key atoms and their intermediate binding between two key atoms.

RESULTS: The substructure pair descriptor (SPAD) represents peptides as the combination of forty-nine types of key substructures and the sequence of amino acid residues between two substructures. The size of the key substructures is larger and the length of the sequence is longer than traditional descriptors. Similarity searches on C5a inhibitor data set and kinase inhibitor data set showed that order of inhibitors become three times higher by representing peptides with SPAD, respectively. Comparing scope of each descriptor shows that SPAD captures different properties from APH.

CONCLUSION: QSAR/QSPR for peptides is helpful for designing various types of drugs such as kinase inhibitor and antigen. SPAD is a novel and powerful descriptor for various types of peptides. Accuracy of QSAR/QSPR becomes higher by describing peptides with SPAD.

References

  1. J Chem Inf Model. 2010 Apr 26;50(4):487-99 - PubMed
  2. Drug Discov Today. 2006 Dec;11(23-24):1046-53 - PubMed
  3. Curr Top Med Chem. 2008;8(18):1628-55 - PubMed
  4. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):438-42 - PubMed
  5. J Biol Phys. 2002 Jun;28(2):183-94 - PubMed
  6. Protein Eng. 1999 Jan;12(1):3-9 - PubMed
  7. J Comput Aided Mol Des. 1994 Dec;8(6):635-52 - PubMed
  8. Environ Health Perspect. 1996 Oct;104 Suppl 5:1031-40 - PubMed
  9. Science. 1960 Oct 21;132(3434):1115-8 - PubMed

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