Description:
In bioinformatics or chemoinformatics, we always need data mining of support vector machines (SVMs) for its large databases. Kernels play an important role in SVMs. Thus it is very necessary to list all the kernels of SVMs that we currently use.
Description:
In bioinformatics or chemoinformatics, we always need data mining of support vector machines (SVMs) for its large databases. Kernels play an important role in SVMs. Thus it is very necessary to list all the kernels of SVMs that we currently use.
Description:
This article presents a new multidimensional descent method for solving global optimization problems with box-constraints. This is a hybrid method where local search method is used for a local descent and global search is used for further multidimensional search on the subsets of intersection of cones generated by the local search method and the feasible region. The discrete gradient method is used for local search and the cutting angle method is used for global search. Two-and three-dimensional cones are used for the global search. Such an approach allows one, as a rule, to escape local minimizers which are not global ones. The proposed method is local optimization method with strong global search properties. We present results of numerical experiments using both smooth and non-smooth global optimization test problems. These results demonstrate that the proposed algorithm allows one to find a global or a near global minimizer.
An effective simulated annealing refined replica exchange Markov chain Monte Carlo algorithm for the infectious disease model of H1N1 influenza pandemic
Description:
This paper is concerned with a computational algorithm for fitting a deterministic MSEIRS (immune-susceptible-exposed-infectious-recovered-susceptible) epidemic model for the transmission of influenza (H1N1) to mortality data. The model-fitting is carried out using a simulated annealing refined replica exchange Markov chain Monte Carlo algorithm. The effectiveness of the algorithm is illustrated using the triple wave data from five English towns collected during the 1918 ~ 1919 influenza pandemic. Numerical results show that the replica exchange (refined by simulated annealing) sampling technique is superior to other existing sampling techniques such as the Gibbs sampling technique, the Metropolis-Hastings sampling technique, the Multiple-try Metropolis technique for the Markov chain Monte Carlo computation. The algorithm presented in this paper has great promise to be used for carrying out some numerical computations of the current complex 2009 ∼ 2010 influenza pandemic.
Description:
This paper is concerned with a computational algorithm for fitting a deterministic MSEIRS (immune-susceptible-exposed-infectious-recovered-susceptible) epidemic model for the transmission of influenza (H1N1) to mortality data. The model-fitting is carried out using a simulated annealing refined replica exchange Markov chain Monte Carlo algorithm. The effectiveness of the algorithm is illustrated using the triple wave data from five English towns collected during the 1918 ~ 1919 influenza pandemic. Numerical results show that the replica exchange (refined by simulated annealing) sampling technique is superior to other existing sampling techniques such as the Gibbs sampling technique, the Metropolis-Hastings sampling technique, the Multiple-try Metropolis technique for the Markov chain Monte Carlo computation. The algorithm presented in this paper has great promise to be used for carrying out some numerical computations of the current complex 2009 ∼ 2010 influenza pandemic.
Description:
In computational chemistry or crystallography, we always meet the problem that requires distributing N particles in one square unit with the minimal neighbor distance. Sometimes this problem is with special or complex constraints. This short article will build a molecular optimization model for the problem, and then will show one example of the application of this model.
Description:
In computational chemistry or crystallography, we always meet the problem that requires distributing N particles in one square unit with the minimal neighbor distance. Sometimes this problem is with special or complex constraints. This short article will build a molecular optimization model for the problem, and then will show one example of the application of this model.
Description:
This article presents a comparative analysis of two methods of global optimization: the simulated annealing method and a method based on a combination of the cutting angle method and a local search. This analysis is carried out using results of numerical experiments. These results demonstrate that the combined method is more effective than the simulated annealing method.
Description:
This article presents a comparative analysis of two methods of global optimization: the simulated annealing method and a method based on a combination of the cutting angle method and a local search. This analysis is carried out using results of numerical experiments. These results demonstrate that the combined method is more effective than the simulated annealing method.
Description:
Background: Prion diseases are fatal and infectious neurodegenerative diseases affecting humans and animals. Rabbits are one of the few mammalian species reported to be resistant to infection from prion diseases isolated from other species (I. Vorberg et al., Journal of Virology 77 (3) (2003) 2003-2009). Thus the study of rabbit prion protein structure to obtain insight into the immunity of rabbits to prion diseases is very important. Findings: The paper is a straight forward molecular dynamics simulation study of wild-type rabbit prion protein (monomer cellular form) which apparently resists the formation of the scrapie form. The comparison analyses with human and mouse prion proteins done so far show that the rabbit prion protein has a stable structure. The main point is that the enhanced stability of the C-terminal ordered region especially helix 2 through the D177-R163 salt-bridge formation renders the rabbit prion protein stable. The salt bridge D201-R155 linking helixes 3 and 1 also contributes to the structural stability of rabbit prion protein. The hydrogen bond H186-R155 partially contributes to the structural stability of rabbit prion protein. Conclusions: Rabbit prion protein was found to own the structural stability, the salt bridges D177-R163, D201-R155 greatly contribute and the hydrogen bond H186-R155 partially contributes to this structural stability. The comparison of the structural stability of prion proteins from the three species rabbit, human and mouse showed that the human and mouse prion protein structures were not affected by the removing these two salt bridges. Dima et al. (Biophysical Journal 83 (2002) 1268-1280 and Proceedings of the National Academy of Sciences of the United States of America 101 (2004) 15335-15340) also confirmed this point and pointed out that "correlated mutations that reduce the frustration in the second half of helix 2 in mammalian prion proteins could inhibit the formation of PrPSc".
Description:
Background: Prion diseases are fatal and infectious neurodegenerative diseases affecting humans and animals. Rabbits are one of the few mammalian species reported to be resistant to infection from prion diseases isolated from other species (I. Vorberg et al., Journal of Virology 77 (3) (2003) 2003-2009). Thus the study of rabbit prion protein structure to obtain insight into the immunity of rabbits to prion diseases is very important. Findings: The paper is a straight forward molecular dynamics simulation study of wild-type rabbit prion protein (monomer cellular form) which apparently resists the formation of the scrapie form. The comparison analyses with human and mouse prion proteins done so far show that the rabbit prion protein has a stable structure. The main point is that the enhanced stability of the C-terminal ordered region especially helix 2 through the D177-R163 salt-bridge formation renders the rabbit prion protein stable. The salt bridge D201-R155 linking helixes 3 and 1 also contributes to the structural stability of rabbit prion protein. The hydrogen bond H186-R155 partially contributes to the structural stability of rabbit prion protein. Conclusions: Rabbit prion protein was found to own the structural stability, the salt bridges D177-R163, D201-R155 greatly contribute and the hydrogen bond H186-R155 partially contributes to this structural stability. The comparison of the structural stability of prion proteins from the three species rabbit, human and mouse showed that the human and mouse prion protein structures were not affected by the removing these two salt bridges. Dima et al. (Biophysical Journal 83 (2002) 1268-1280 and Proceedings of the National Academy of Sciences of the United States of America 101 (2004) 15335-15340) also confirmed this point and pointed out that "correlated mutations that reduce the frustration in the second half of helix 2 in mammalian prion proteins could inhibit the formation of PrPSc".
Description:
In recent years large-scale global optimization (GO) problems have drawn considerable attention. These problems have many applications, in particular in data mining and biochemistry. Numerical methods for GO are often very time consuming and could not be applied for high-dimensional non-convex and / or non-smooth optimization problems. The thesis explores reasons why we need to develop and study new algorithms for solving large-scale GO problems .... The thesis presents several derivative-free hybrid methods for large scale GO problems. These methods do not guarantee the calculation of a global solution; however, results of numerical experiments presented in this thesis demonstrate that they, as a rule, calculate a solution which is a global one or close to it. Their applications to data mining problems and the protein folding problem are demonstrated.
Description:
In recent years large-scale global optimization (GO) problems have drawn considerable attention. These problems have many applications, in particular in data mining and biochemistry. Numerical methods for GO are often very time consuming and could not be applied for high-dimensional non-convex and / or non-smooth optimization problems. The thesis explores reasons why we need to develop and study new algorithms for solving large-scale GO problems .... The thesis presents several derivative-free hybrid methods for large scale GO problems. These methods do not guarantee the calculation of a global solution; however, results of numerical experiments presented in this thesis demonstrate that they, as a rule, calculate a solution which is a global one or close to it. Their applications to data mining problems and the protein folding problem are demonstrated.
Description:
Prion protein (PrP) has two regions: unstructured region PrP(1-120) and structured region PrP(119-231). In the structured region, there are many segments which have the property of amyloid fibril formation. By theoretical calculations, PrP(126-133), PrP(137-143), PrP(170-175), PrP(177-182), PrP(211-216) have the amyloid fibril forming property. PrP(142-166) has a X-ray crystallography experimental
Description:
Prion protein (PrP) has two regions: unstructured region PrP(1-120) and structured region PrP(119-231). In the structured region, there are many segments which have the property of amyloid fibril formation. By theoretical calculations, PrP(126-133), PrP(137-143), PrP(170-175), PrP(177-182), PrP(211-216) have the amyloid fibril forming property. PrP(142-166) has a X-ray crystallography experimental
Description:
For amyloid fibril cross-β structures of Aβ human protein, we find theoretical calculations are agreeing with laboratory X-ray crystallography experiments. This mini article summarized mathematical formulas of amyloid fibril cross-β structures of segments of human Aβ protein. These formulas are accurate and correct some data in the Protein Data Bank (PDB). However, more mathematical formulas for core Chains AB (PDB IDs: 3OW9, 3PZZ, 2OKZ), or ABGH (PDB IDs: 3OVJ, 2Y3J, 2Y3K, 2Y3L) (or ABCD (PDB ID: 2ONA)) are still needed to present and optimize.
Description:
For amyloid fibril cross-β structures of Aβ human protein, we find theoretical calculations are agreeing with laboratory X-ray crystallography experiments. This mini article summarized mathematical formulas of amyloid fibril cross-β structures of segments of human Aβ protein. These formulas are accurate and correct some data in the Protein Data Bank (PDB). However, more mathematical formulas for core Chains AB (PDB IDs: 3OW9, 3PZZ, 2OKZ), or ABGH (PDB IDs: 3OVJ, 2Y3J, 2Y3K, 2Y3L) (or ABCD (PDB ID: 2ONA)) are still needed to present and optimize.
Description:
Unlike bacteria and viruses, which are based on DNA and RNA, prions are unique as disease-causing agents since they are misfolded proteins. Prion diseases are called "protein structural conformational diseases. This monograph is the book on molecular dynamics (MD) simulations nearly for all the known normal prion protein (PrPC) PDB entries in the Protein Data Bank (PDB) and associations. Pig is a species that is largely resistant to prions, and chicken, turtles, frogs are species resisting prion infection too firstly, this book will address all PrP strong immunity species (such as rabbits, dogs, horses, water buffaloes, pigs, chicken, turtles, frogs), compared with high susceptibility species. Other PrP models and doppel models are also MD studied in this book. Secondly, all the mutants of mouse PrP and human PrP are well studied by this book. Mouse mutations in the 2-2 loop and the C-terminal will bring clear structures with highly and clearly ordered loop structures. Human mutations will cause prion diseases such as Creutzfeldt-Jakob diseases (CJDs), Gerstmann-Sträussler-Scheinker (GSS) syndrome, fatal familial insomnia (FFI), etc. Deep MD analyses of mouse and human mutants are done in this book. Thirdly, PrP binding with antibodies/compounds etc. is well MD studied in this book. The informatics of potential antiprion drugs known will be revealed. Lastly, cross- structure PrP peptides are well studied. This book is ideal for practical computing staff in the fields of computational physics, computational biology, computational chemistry, biomedicine, bioinformatics, cheminformatics, materials, applied mathematics and theoretical physics, information technology, operations research, biostatistics, etc. As an accessible introduction to these fields, this book is also ideal as a teaching material for students.
Description:
Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and goats, cattle, deer and elk, and humans. But for rabbits, studies have shown that they have a low susceptibility to be infected by prion diseases. This paper does molecular dynamics (MD) studies of rabbit NMR structures (of the wild type and its two mutants of two surface residues), in order to understand the specific mechanism of rabbit prion proteins (RaPrPC). Protein surface electrostatic charge distributions are specially focused to analyze the MD trajectories. This paper can conclude that surface electrostatic charge distributions indeed contribute to the structural stability of wild-type RaPrPC; this may be useful for the medicinal treatment of prion diseases.
Description:
Prion diseases such as Creutzfeldt-Jakob disease, variant Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, Fatal Familial Insomnia, Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (or ‘mad-cow’ disease) and chronic wasting disease in cattle are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. However, by now there have not been some effective therapeutic approaches to treat all these prion diseases. In 2008, canine mammals including dogs (canis familials) were the first time academically reported to be resistant to prion diseases (Vaccine 26: 2601-2614 (2008)). Thus, it is very worth studying the molecular structures of dog prion protein to obtain insights into the immunity of dogs to prion diseases. This paper studies the molecular structural dynamics of wild-type dog prion protein. The comparison analyses with rabbit prion protein show that the dog prion protein has stable molecular structures whether under neutral or low pH environments. We also find that the salt bridges such as D177-R163 contribute to the structural stability of wild-type rabbit prion protein under neutral pH environment.