Microarrays for Amino Acid Analysis and Protein Sequencing [PDF]
arXiv, 1999 A method is described where the aminoacyl-tRNA synthetase system is used to create very small devices for quantitative analysis of the amino acids that occur in proteins. The basis of the method is that each of the 20 synthetases and/or a tRNA specific for a different amino acid is separated spatially (e.g. in tiny chambers or on a surface).
arxiv
BMC Research Notes, 2010 Background NruI and Sbo13I are restriction enzyme isoschizomers with the same recognition sequence 5' TCG↓CGA 3' (cleavage as indicated↓). Here we report the cloning of NruI and Sbo13I restriction-modification (R-M) systems in E. coli.
Benner Jack +4 more
doaj +1 more source
The response of amino acid frequencies to directional mutation pressure in mitochondrial genome sequences is related to the physical properties of the amino acids and to the structure of the genetic code [PDF]
arXiv, 2005 The frequencies of A, C, G and T in mitochondrial DNA vary among species due to unequal rates of mutation between the bases. The frequencies of bases at four-fold degenerate sites respond directly to mutation pressure. At 1st and 2nd positions, selection reduces the degree of frequency variation.
arxiv
A modular Fibonacci sequence in proteins [PDF]
arXiv, 2004 Protein-fragment seqlets typically feature about 10 amino acid residue positions that are fixed to within conservative substitutions but usually separated by a number of prescribed gaps with arbitrary residue content. By quantifying a general amino acid residue sequence in terms of the associated codon number sequence, we have found a precise modular ...
arxiv
Data on Rad51 amino acid sequences from higher and lower eukaryotic model organisms and parasites
Data in Brief, 2017 This paper contains data related to the research article titled “Characterization of the recombination activities of the Entamoeba histolytica Rad51 recombinase” (Kelso et al., in press) [1].
Andrew A. Kelso +3 more
doaj +1 more source
Reading the three-dimensional structure of a protein from its amino acid sequence [PDF]
arXiv, 2000 While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of a protein whose sequence is known. This situation is not particularly satisfactory, in keeping with the fact that
arxiv
Classification of Macromolecule Type Based on Sequences of Amino Acids Using Deep Learning [PDF]
arXiv, 2019 The classification of amino acids and their sequence analysis plays a vital role in life sciences and is a challenging task. This article uses and compares state-of-the-art deep learning models like convolution neural networks (CNN), long short-term memory (LSTM), and gated recurrent units (GRU) to solve macromolecule classification problems using ...
arxiv
Filovirus Glycoprotein Sequence, Structure and Virulence [PDF]
arXiv, 2014 Leading Ebola subtypes exhibit a wide mortality range, here explained at the molecular level by using fractal hydropathic scaling of amino acid sequences based on protein self-organized criticality. Specific hydrophobic features in the hydrophilic mucin-like domain suffice to account for the wide mortality range.
arxiv
Multiple sequence alignments of partially coding nucleic acid sequences
BMC Bioinformatics, 2005 Background High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data.
Fried Claudia +3 more
doaj +1 more source
A Mean-Field Description of Protein Folding: Evolutional Conservation of Hydrophobicity Profile and Folding Nuclei [PDF]
arXiv, 2006 Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D (3-dimensional) information of the structure is considered and it is found that a 3D hydrophobicity profile is essential ...
arxiv