Replica Exchange Aided Wang-Landau Algorithm for Protein Folding - 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 Aided Wang-Landau Algorithm for Protein Folding write by Liang Han. This book was released on 2007. Replica Exchange Aided Wang-Landau Algorithm for Protein Folding available in PDF, EPUB and Kindle.
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.
Applications of Replica Exchange Method in All-atom Protein Folding Simulations
Applications of Replica Exchange Method in All-atom Protein Folding Simulations - 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 Applications of Replica Exchange Method in All-atom Protein Folding Simulations write by Thu Zar Wai Lwin. This book was released on 2005. Applications of Replica Exchange Method in All-atom Protein Folding Simulations available in PDF, EPUB and Kindle.
Applied Computer-Aided Drug Design: Models and Methods
Applied Computer-Aided Drug Design: Models and Methods - 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 Applied Computer-Aided Drug Design: Models and Methods write by Igor José dos Santos Nascimento. This book was released on 2023-12-08. Applied Computer-Aided Drug Design: Models and Methods available in PDF, EPUB and Kindle. Designing and developing new drugs is an expensive and time-consuming process, and there is a need to discover new tools or approaches that can optimize this process. Applied Computer-Aided Drug Design: Models and Methods compiles information about the main advances in computational tools for discovering new drugs in a simple and accessible language for academic students to early career researchers. The book aims to help readers understand how to discover molecules with therapeutic potential by bringing essential information about the subject into one volume. Key Features · Presents the concepts and evolution of classical techniques, up to the use of modern methods based on computational chemistry in accessible format. · Gives a primer on structure- and ligand-based drug design and their predictive capacity to discover new drugs. · Explains theoretical fundamentals and applications of computer-aided drug design. · Focuses on a range of applications of the computations tools, such as molecular docking; molecular dynamics simulations; homology modeling, pharmacophore modeling, quantitative structure-activity relationships (QSAR), density functional theory (DFT), fragment-based drug design (FBDD), and free energy perturbation (FEP). · Includes scientific reference for advanced readers Readership Students, teachers and early career researchers.
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes - 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 Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes write by Adam Liwo. This book was released on 2013-07-17. Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes available in PDF, EPUB and Kindle. Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.
