Journal ArticleDOI
Is it Possible to Analyze DNA and Protein Sequences by the Methods of Digital Signal Processing
TLDR
It is shown that the multiple cross spectrum of functionally related sequences exhibits significant peak frequencies, and it is conjecture that the peak frequencies in the multipleCross spectrum of sequences with the same boilogical function are related to this biological function.Abstract:
Informational content of linear macromolecules (DNA, RNA, and proteins) is analyzed by the method of digital signal processing. Each element (amino acid or nucleotide) of macromolecules is represented by the corresponding value of electron-ion interaction potential. This numerical representation of the primary structure of macromolecules is subjected to digital signal processing in order to extract the information corresponding to biological function. It is shown that the multiple cross spectrum of functionally related sequences exhibits significant peak frequencies. In the case of functionally unrelated sequences such peaks were not found. Peak frequencies are different for different biological functions. Based on this, we conjecture that the peak frequencies in the multiple cross spectrum of sequences with the same boilogical function are related to this biological function.read more
Citations
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Characterization of conserved properties of hemagglutinin of H5N1 and human influenza viruses: possible consequences for therapy and infection control
Veljko Veljkovic,Nevena Veljkovic,Claude P. Muller,Sybille Muller,Sanja Glisic,Vladimir Perovic,Heinz Kohler +6 more
TL;DR: Comparison of informational and structural properties of the hemagglutinin (HA) of H5N1 virus and human influenza virus subtypes may help to better understand the interaction of influenza virus with its receptor(s) and to identify new therapeutic targets for drug development.
Journal ArticleDOI
A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes.
Frédéric Cadet,Nicolas K. Fontaine,Guangyue Li,Joaquin Sanchis,Matthieu Ng Fuk Chong,Rudy Pandjaitan,Iyanar Vetrivel,Bernard Offmann,Manfred T. Reetz,Manfred T. Reetz +9 more
TL;DR: This work presents an innovative sequence-activity relationship (innov’SAR) methodology based on digital signal processing combining wet-lab experimentation and computational protein design and illustrates the application in the case of improving the enantioselectivity of an epoxide hydrolase from Aspergillus niger.
Journal ArticleDOI
SFAPS: An R package for structure/function analysis of protein sequences based on informational spectrum method
TL;DR: The R package SFAPS has been developed for structure/function analysis of protein sequences based on information spectrum method, which obtains the characteristic frequency of a particular protein interaction after computing the Discrete Fourier Transform for protein sequences.
Journal ArticleDOI
Criteria for confirming sequence periodicity identified by Fourier transform analysis: application to GCR2, a candidate plant GPCR?
Christopher J. R. Illingworth,Kevin E. B. Parkes,Christopher R. Snell,Philip M. Mullineaux,Christopher A. Reynolds +4 more
TL;DR: Application of the Fourier transform algorithm to the G CR2 family revealed strongly predicted seven fold periodicity in hydrophobicity, suggesting why GCR2 has been reported to be a GPCR, despite negative indications in most transmembrane prediction algorithms.
Journal ArticleDOI
CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences
TL;DR: As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server, which are probable to be related with the protein feature that the specific amino acid index represents.
References
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Journal ArticleDOI
Regulatory Sequences Involved in the Promotion and Termination of RNA Transcription
Martin Rosenberg,Donald L. Court +1 more
Journal ArticleDOI
Similar Amino Acid Sequences: Chance or Common Ancestry?
TL;DR: The systemic comparison of every newly determined amino acid sequence with all other known sequences may allow a complete reconstruction of the evolutionary events leading to contemporary proteins, but sometimes the surviving similarities are so vague that even computer-based sequence comparisons procedures are unable to validate relationships.
Journal ArticleDOI
The structure of eight distinct cloned human leukocyte interferon cDNAs.
David V. Goeddel,David W. Leung,Thomas J. Dull,Mitchell Gross,Richard M. Lawn,Russell McCandliss,Peter H. Seeburg,Axel Ullrich,Elizabeth Mcleod Yelverton,Patrick W. Gray +9 more
TL;DR: Eight classes of human leukocyte interferon cDNA clones have been identified in a cDNA library prepared from a myeloblastoid cell line and nucleotide sequences demonstrate that the multiple human LeIFN genes code for a family of homologous, yet distinct proteins.
Journal ArticleDOI
Activation of ki-ras2 gene in human colon and lung carcinomas by two different point mutations
Daniel J. Capon,Peter H. Seeburg,John P. McGrath,Joel S. Hayflick,Ursula Edman,Arthur D. Levinson,David V. Goeddel +6 more
TL;DR: Kirsten (Ki)-ras cDNA clones were prepared from human lung and colon carcinoma cell lines expressing an activated c-Ki-ras2 gene and DNA sequence analysis and transfection studies indicate that different point mutations at the same codon can activate the gene.
Journal ArticleDOI
Nucleotide sequence of an avian sarcoma virus oncogene (src) and proposed amino acid sequence for gene product.
TL;DR: It appears that a single viral protein is responsible for both the initiation and maintenance of neoplastic transformation by avian sarcoma virus.