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Prediction of secondary protein structure with binary coding patterns of amino acid and nucleotide physicochemical properties


Štambuk, Nikola; Konjevoda, Paško
Prediction of secondary protein structure with binary coding patterns of amino acid and nucleotide physicochemical properties // International Journal of Quantum Chemistry, 92 (2003), 2; 123-134 (međunarodna recenzija, članak, znanstveni)


Naslov
Prediction of secondary protein structure with binary coding patterns of amino acid and nucleotide physicochemical properties

Autori
Štambuk, Nikola ; Konjevoda, Paško

Izvornik
International Journal of Quantum Chemistry (0020-7608) 92 (2003), 2; 123-134

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
protein fold; secondary structure; prediction; error-correcting code; genetic code; nucleotides; amino acids

Sažetak
We present binary coding algorithm for the alpha- and beta-protein fold prediction. The method links amino acid molecular polarity patterns and physicochemical properties of nucleotide bases coded by means of a binary addresses. Primary sequences that define secondary protein structure were analyzed with respect to the symbolic oligopeptides (SO) obtained by the reduction of the 20 amino acid letter alphabet into a binary alphabet of nonpolar group 0 (W, C, I, F, M, V, L, Y) and polar group 1 (Q, R, H, K, N, E, D, S, G, T, A, P). The groups were extracted from the Grantham polarity scale with the clustering around medoids procedure. The transformation of protein strings into binary coding patterns of the polar and nonpolar amino acid groups reduced analyzed elements within the protein motif of length n by the factor of 10^n. SMO learning algorithm for the support vector machines was applied to classify alpha-helices and beta-strands. It was shown that the relative frequencies of binary hexapeptides classify all 174 nonhomologous alpha- and beta-protein folds from the Jpred database with 100% accuracy. The results of 10-fold cross-validation and leave-one-out test were 86.78%. Classification tree confirmed the results of SMO analysis and correctly classified 100% of the folds by means of 9 binary hexapeptides. Linear block triple-check code was proposed for the description of hexapeptide patterns. The presented method enables simple, quick, and accurate prediction of alpha- and beta-protein folding types from the primary amino acid and nucleotide sequences on a personal computer. Our results imply that few amino acid polarity patterns specified by the nucleotide physicochemical properties describe basic protein folding types with >90% accuracy.

Izvorni jezik
Engleski

Znanstvena područja
Temeljne medicinske znanosti



POVEZANOST RADA


Projekt / tema
0098097

Ustanove
Institut "Ruđer Bošković", Zagreb

Profili:

Avatar Url Paško Konjevoda (autor)

Avatar Url Nikola Štambuk (autor)

Citiraj ovu publikaciju

Štambuk, Nikola; Konjevoda, Paško
Prediction of secondary protein structure with binary coding patterns of amino acid and nucleotide physicochemical properties // International Journal of Quantum Chemistry, 92 (2003), 2; 123-134 (međunarodna recenzija, članak, znanstveni)
Štambuk, N. & Konjevoda, P. (2003) Prediction of secondary protein structure with binary coding patterns of amino acid and nucleotide physicochemical properties. International Journal of Quantum Chemistry, 92 (2), 123-134.
@article{article, year = {2003}, pages = {123-134}, keywords = {protein fold, secondary structure, prediction, error-correcting code, genetic code, nucleotides, amino acids}, journal = {International Journal of Quantum Chemistry}, volume = {92}, number = {2}, issn = {0020-7608}, title = {Prediction of secondary protein structure with binary coding patterns of amino acid and nucleotide physicochemical properties}, keyword = {protein fold, secondary structure, prediction, error-correcting code, genetic code, nucleotides, amino acids} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus


Uključenost u ostale bibliografske baze podataka:


  • Excerpta Medica
  • Index Medicus