Comparative Modeling and Protein-like Features of Hydrophobic-polar Models on a Two-dimensional Lattice - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Comparative Modeling and Protein-like Features of Hydrophobic-polar Models on a Two-dimensional Lattice write by Sergio Moreno Hernandez. This book was released on 2012. Comparative Modeling and Protein-like Features of Hydrophobic-polar Models on a Two-dimensional Lattice available in PDF, EPUB and Kindle. Lattice models of proteins have been extensively used to study protein thermodynamics, folding dynamics and evolution. Our study considers two different hydrophobic-polar (HP) models on the two-dimensional square lattice: the purely HP model and a model where a compactness-favoring term is added. We exhaustively enumerate all the possible structures in our models and perform the study of their corresponding folds, HP arrangements in space and shapes. The two models considered differ greatly in their numbers of structures, folds, arrangements, and shapes. Despite their differences both lattice models have distinctive protein-like features: (1) Shapes are compact in both models, especially when a compactness-favoring energy term is added. (2) The residue composition is independent of the chain length and is very close to 50% hydrophobic in both models, as we observe in real proteins. (3) Comparative modeling works well in both models, particularly in the more compact one. The fact that our models show protein-like features suggests that lattice models incorporate the fundamental physical principles of proteins. Our work supports the use of lattice models to study questions about proteins that require exactness and extensive calculations, such as protein design and evolution, which are often too complex and computationally demanding to be addressed with more detailed models.
Lecture Notes in Computational Intelligence and Decision Making
Lecture Notes in Computational Intelligence and Decision Making - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Lecture Notes in Computational Intelligence and Decision Making write by Volodymyr Lytvynenko. This book was released on 2019-07-23. Lecture Notes in Computational Intelligence and Decision Making available in PDF, EPUB and Kindle. Information and computer technologies for data analysis and processing in various fields of data mining and machine learning generates the conditions for increasing the effectiveness of information processing by making it faster and more accurate. The book includes 49 scientific papers presenting the latest research in the fields of data mining, machine learning and decision-making. Divided into three sections: “Analysis and Modeling of Complex Systems and Processes”; “Theoretical and Applied Aspects of Decision-Making Systems”; and “Computational Intelligence and Inductive Modeling”, the book is of interest to scientists and developers in the field.
A Metaheuristic Approach to Protein Structure Prediction
A Metaheuristic Approach to Protein Structure Prediction - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook A Metaheuristic Approach to Protein Structure Prediction write by Nanda Dulal Jana. This book was released on 2018-03-05. A Metaheuristic Approach to Protein Structure Prediction available in PDF, EPUB and Kindle. This book introduces characteristic features of the protein structure prediction (PSP) problem. It focuses on systematic selection and improvement of the most appropriate metaheuristic algorithm to solve the problem based on a fitness landscape analysis, rather than on the nature of the problem, which was the focus of methodologies in the past. Protein structure prediction is concerned with the question of how to determine the three-dimensional structure of a protein from its primary sequence. Recently a number of successful metaheuristic algorithms have been developed to determine the native structure, which plays an important role in medicine, drug design, and disease prediction. This interdisciplinary book consolidates the concepts most relevant to protein structure prediction (PSP) through global non-convex optimization. It is intended for graduate students from fields such as computer science, engineering, bioinformatics and as a reference for researchers and practitioners.
Replica-exchange Wang-landau Simulations of Lattice Proteins for the Understanding of the Protein Folding Problem
Replica-exchange Wang-landau Simulations of Lattice Proteins for the Understanding of the Protein Folding Problem - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Replica-exchange Wang-landau Simulations of Lattice Proteins for the Understanding of the Protein Folding Problem write by Guangjie Shi. This book was released on 2016. Replica-exchange Wang-landau Simulations of Lattice Proteins for the Understanding of the Protein Folding Problem available in PDF, EPUB and Kindle. Protein folding is studied within the context of two coarse-grained lattice models that separate all amino acids into only a few types. The hydrophobic-polar (HP) model is a simplified lattice protein model for simulating protein folding and for understanding many biological problems of interest. In this work, an "improved" model, the semi-flexible H0P model, was proposed by introducing a new type of "neutral" monomer, "0", i.e., neither hydrophobic nor polar and also taking into consideration the stiffness of bonds connecting monomers. Even though both models are highly simplified protein models, finding the lowest energy conformations and determining the density of states are extremely difficult. We applied replica-exchange Wang-Landau sampling with appropriate trial moves for determining the density of states of multiple HP and H0P proteins, from which the thermodynamic properties such as specific heat can be calculated. Moreover, we developed a heuristic method for determining the ground state degeneracy of lattice proteins, based on multicanonical sampling. It is applied during comprehensive studies of single-site mutations in specific lattice proteins with different sequences. The effects in which we are interested include structural changes in ground states, changes of ground state energy, degeneracy, and thermodynamic properties of the system. With respect to mutations, both extremely sensitive and insensitive positions in the protein sequence have been found. That is, ground state energies and degeneracies, as well as other thermodynamic and structural quantities may be either largely unaffected or may change significantly due to mutation. Moreover, comparison between the HP model and the semi-flexible H0P model have been performed based on two real proteins: Crambin and Ribonuclease A. We found that, compared with the HP model, the semi-flexible H0P model possesses significantly reduced ground state degeneracy, and rich folding signals as the proteins rearranging into native states from very compact structures at low temperatures. We calculated the free energy vs end-to-end distance as a function of temperature. The HP model shows a relatively shallow folding funnel and flat free energy minimum, reflecting the high degeneracy of the ground state. In contrast, the semi-flexible H0P model has a well developed, rough free energy funnel with a low degeneracy ground state. In both cases, folding funnels are asymmetric with temperature dependent shape.
Encyclopedia of Chemical Physics and Physical Chemistry
Encyclopedia of Chemical Physics and Physical Chemistry - read free eBook in online reader or directly download on the web page. Select files or add your book in reader. Download and read online ebook Encyclopedia of Chemical Physics and Physical Chemistry write by John H. Moore. This book was released on 2023-07-03. Encyclopedia of Chemical Physics and Physical Chemistry available in PDF, EPUB and Kindle. The Encyclopedia of Physical Chemistry and Chemical Physics introduces possibly unfamiliar areas, explains important experimental and computational techniques, and describes modern endeavors. The encyclopedia quickly provides the basics, defines the scope of each subdiscipline, and indicates where to go for a more complete and detailed explanation. Particular attention has been paid to symbols and abbreviations to make this a user-friendly encyclopedia. Care has been taken to ensure that the reading level is suitable for the trained chemist or physicist. The encyclopedia is divided in three major sections: FUNDAMENTALS: the mechanics of atoms and molecules and their interactions, the macroscopic and statistical description of systems at equilibrium, and the basic ways of treating reacting systems. The contributions in this section assume a somewhat less sophisticated audience than the two subsequent sections. At least a portion of each article inevitably covers material that might also be found in a modern, undergraduate physical chemistry text. METHODS: the instrumentation and fundamental theory employed in the major spectroscopic techniques, the experimental means for characterizing materials, the instrumentation and basic theory employed in the study of chemical kinetics, and the computational techniques used to predict the static and dynamic properties of materials. APPLICATIONS: specific topics of current interest and intensive research. For the practicing physicist or chemist, this encyclopedia is the place to start when confronted with a new problem or when the techniques of an unfamiliar area might be exploited. For a graduate student in chemistry or physics, the encyclopedia gives a synopsis of the basics and an overview of the range of activities in which physical principles are applied to chemical problems. It will lead any of these groups to the salient points of a new field as rapidly as possible and gives pointers as to where to read about the topic in more detail.
