ABSTRACT
We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in the literature.
Subject(s)
Computational Biology/methods , Sequence Alignment , Algorithms , Models, Statistical , Probability , SoftwareABSTRACT
We predict the potential active and catalytic sites, the transition state and how it is stabilized, and the mechanism of rihC ribonucleoside hydrolase of E. coli. Our approach is based on well-known primary sequence analysis techniques. A canonically associated extreme value distribution is used to assess the significance of the prediction. Parameters for the extreme value distribution are computed directly from data. Our practical approach is consistent with known results in the literature. We obtain BLOSUM matrices in a way that is intrinsically tied to the data base, and we employ user-friendly techniques that should be applicable to a range of medically significant scenarios.
Subject(s)
Escherichia coli Proteins/chemistry , Escherichia coli Proteins/genetics , Escherichia coli/enzymology , Escherichia coli/genetics , N-Glycosyl Hydrolases/chemistry , N-Glycosyl Hydrolases/genetics , Sequence Analysis, Protein/statistics & numerical data , Algorithms , Catalytic Domain/genetics , Computational Biology , Crithidia fasciculata/enzymology , Crithidia fasciculata/genetics , Genes, BacterialABSTRACT
We develop a systems based model for prostate cancer, as a sub-system of the organism. We accomplish this in two stages. We first start with a general ODE that includes organism response terms. Then, to account for normally observed spatial diffusion of cell populations, the ODE is extended to a PDE that includes spatial terms. Numerical solutions of the full PDE are provided, and are indicative of traveling wave fronts. This motivates the use of a well known transformation to derive a canonically related (non-linear) system of ODEs for traveling wave solutions. For biological feasibility, we show that the non-negative cone for the traveling wave system is time invariant. We also prove that the traveling waves have a unique global attractor. Biologically, the global attractor would be the limit for the avascular tumor growth. We conclude with comments on clinical implications of the model.
Subject(s)
Cell Transformation, Neoplastic/pathology , Models, Biological , Precancerous Conditions/pathology , Precancerous Conditions/physiopathology , Prostatic Neoplasms/pathology , Prostatic Neoplasms/physiopathology , Stem Cells/pathology , Stem Cells/physiology , Computer Simulation , Humans , MaleABSTRACT
The study of electron/proton transport in alpha-helix sections of proteins have illustrated the existence of soliton-like mechanisms. Recently, Ciblis and Cosic extended investigation to the existence of possible like soliton-type mechanisms in other parts of the protein. They used Quantum Hamiltonian analysis to investigate. In this paper, we investigate the same problem but we use Classical Hamiltonian analysis in our investigation.
