Search results for "Substitution matrix"
showing 3 items of 3 documents
Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi
2020
Iron is an essential micronutrient for most living beings since it participates as a redox active cofactor in many biological processes including cellular respiration, lipid biosynthesis, DNA replication and repair, and ribosome biogenesis and recycling. However, when present in excess, iron can participate in Fenton reactions and generate reactive oxygen species that damage cells at the level of proteins, lipids and nucleic acids. Organisms have developed different molecular strategies to protect themselves against the harmful effects of high concentrations of iron. In the case of fungi and plants, detoxification mainly occurs by importing cytosolic iron into the vacuole through the Ccc1/V…
Peptide classification using optimal and information theoretic syntactic modeling
2010
Accepted version of an article published in the journal: Pattern Recognition. Published version available on Sciverse: http://dx.doi.org/10.1016/j.patcog.2010.05.022 We consider the problem of classifying peptides using the information residing in their syntactic representations. This problem, which has been studied for more than a decade, has typically been investigated using distance-based metrics that involve the edit operations required in the peptide comparisons. In this paper, we shall demonstrate that the Optimal and Information Theoretic (OIT) model of Oommen and Kashyap [22] applicable for syntactic pattern recognition can be used to tackle peptide classification problem. We advoca…
An ab initio softness metric to measure the similarity between all pairs of amino acids
2010
Abstract The search for quantitative index of similarity between molecular moeties is important for its applications in pharmacology. Similarity is also an important concept in computational biology to measure the exchangeability of an amino acid by another in a protein sequence. In the present work, a distance between two molecules based on local and global softnesses of their fragments is defined. The method proposed is general and could be applied to any molecular library. It is first applied to compute the distance between the 190 pairs of different amino acids in their neutral states. Two amino acids belonging to the one of the biochemical class (aliphatic, sulfur-containing, acidic, ……