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Author : 許茗鈜
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (9 download)
Download or read book Hybrid Branch Model System of Protein Folding Simulation written by 許茗鈜 and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Andrzej Koliński
Publisher : Landes Bioscience
ISBN 13 :
Total Pages : 224 pages
Book Rating : 4.3/5 (91 download)
Download or read book Lattice Models of Protein Folding, Dynamics, and Thermodynamics written by Andrzej Koliński and published by Landes Bioscience. This book was released on 1996 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Irena Roterman-Konieczna
Publisher : Elsevier
ISBN 13 : 1908818255
Total Pages : 241 pages
Book Rating : 4.9/5 (88 download)
Download or read book Protein Folding in Silico written by Irena Roterman-Konieczna and published by Elsevier. This book was released on 2012-10-04 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. Discusses a range of ab initio models for protein structure prediction Introduces a unique model based on experimental observations Describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory
Author : Anna Shumilina
Publisher : Cuvillier Verlag
ISBN 13 : 3736937989
Total Pages : 218 pages
Book Rating : 4.7/5 (369 download)
Download or read book Modeling and Simulation of Protein Folding written by Anna Shumilina and published by Cuvillier Verlag. This book was released on 2011-06-22 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book describes a new mathematical model for intracellular protein folding and the implementation of this model in the form of a novel simulation software. Besides, the related biological, chemical, and physical background, important for understanding and rationalization of the proposed model, is outlined, and a short overview of the best-known methods for protein structure prediction and molecular modeling is given. The first chapter provides a general introduction to the problem, characterizes the chemical structure of proteins, and summarizes amino acid properties, including chirality and ionization behavior. After that, the principles of quantum mechanics and their consequences for the molecular structure are described. The discussion goes over to covalent and hydrogen bonding, as well as to electrostatic and van der Waals interactions. Further, some known facts about the three-dimensional structure of proteins and typical conformations of amino acids are outlined, followed by a quick glance at the hydrophobic effect and the interaction of charged groups with the solvent. Later on the focus is shifted to biological aspects, starting with chaperons and assisted protein folding, mentioning prions, which put into question the popular hypothesis about the global energy minimum of any native structure, and continuing with details of protein synthesis in the cell, which constituted the basis for the proposed model. The chapter finishes with a short description of experimental methods for protein structure prediction and with some information about databases for storage of known protein structures. The second chapter starts with a short overview of the knowledge-based protein structure prediction and ab initio protein folding approaches, then continues with empirical molecular mechanics force fields, typically used for molecular modeling. After that, it describes computation of atomic partial charges with a focus on the procedure of J. Gasteiger and M. Marsili, and proceeds with some models for hydrogen bonding. The chapter ends with a discussion about implicit solvation models. The third chapter describes the new modeling approach and some mathematical theory developed in relation to it. The idea of the model is to simulate a process resembling intracellular cotranslational folding. An attachment of a new residue is performed in a way that the formed peptide group is disposed in the trans conformation, and only the chain twisting about certain single bonds is allowed. Transitions with an energy increase are permitted to a limited extent. Beside the electrostatic and van der Waals interactions, the proposed model incorporates hydrogen and disulfide bonding, solvation effects, and dielectric screening at the protein surface. A general expression connecting interatomic distances and dihedral angles is derived, which resulted in a formulation of the model in the space of molecular torsion angles. Twisting forces are computed analytically and utilized for the improvement of computational efficiency the folding simulations. Besides, equations for dynamics in the space of torsion angles are derived, and a conclusion related to folding pathways is drawn. The last chapter discusses some non-technical details related to the implementation of the proposed model, including a number of developed algorithms, and the resulting simulation software. The chapter ends with a short discussion of simulation results and with an outlook. This book is aimed in the first place to biophysicists and bioinformaticians, but can be also interesting for theoretical chemists, mathematicians, and molecular biologists, since it includes a broad interdisciplinary overview accompanied by unique visualizations, which were performed with the help of the simulation software developed by the author.
Author :
Publisher : Academic Press
ISBN 13 : 0128211350
Total Pages : 552 pages
Book Rating : 4.1/5 (282 download)
Download or read book Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly written by and published by Academic Press. This book was released on 2020-03-18 with total page 552 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field
Author :
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (134 download)
Download or read book Efficient Hybrid Taguchi-Genetic Algorithm for Protein Folding Simulation written by and published by . This book was released on 2008 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Daisuke Kihara
Publisher : Humana
ISBN 13 : 9781071607107
Total Pages : 358 pages
Book Rating : 4.6/5 (71 download)
Download or read book Protein Structure Prediction written by Daisuke Kihara and published by Humana. This book was released on 2021-07-18 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough new edition explores web servers and software for protein structure prediction and modeling that are freely available to the academic community. Taking into account the numerous advances in the computational protein structure prediction/modeling field, the book includes residue-contact prediction via deep learning, a wide variety of protein docking models, as well as cryo-electron microscopy (cryo-EM) techniques. Written by renowned experts in the field and for the highly successful Methods in Molecular Biology series, chapters include the kind of key detail and implementation advice necessary for researchers to achieve optimal results in their own work. Authoritative and fully updated, Protein Structure Prediction, Fourth Edition is a practical and immediately useful guide for biology researchers working toward modeling protein structures./div/div/div/div/div/div/div/div/div/div/div/div/div/div/div/div/divdiv
Author : Wei Zhang
Publisher :
ISBN 13 : 9780542228612
Total Pages : pages
Book Rating : 4.2/5 (286 download)
Download or read book Computational Simulation of Biological Systems written by Wei Zhang and published by . This book was released on 2005 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific understanding as well as the way of studying science has been greatly changed since the advent of computer modeling. Computer simulation has played a central role in bridging theoretical and experimental studies. In this work, computer simulations were applied to explore biological systems on both protein folding and protein structure prediction studies. In the first study, the folding mechanisms of two alanine based helical peptides (Fs-21 peptide and MABA bonded Fs-21 peptide) were investigated by all atom molecular dynamics simulations and compared with experimental results. Multi-phase folding processes were observed for both peptides. Temperature change affected the relative stability of different ensembles. Helix-turn-helix conformation was found to be the most populated state at 300K while the full helix became more stable at low temperature (273K). The turn structure was found to be stabilized mainly by hydrophobic interactions. In the second study, helix-coil transition theory was elaborately tested by both statistical and energetic methods based on simulations of alanine based peptides. A weighted Ising model was proposed, and the model-derived propagation constant agreed very well with the experimental results. Solvation effect and electrostatic interactions were found to be the two main contributors to helix-coil transition. The results challenged the classic helix-coil transition theory by proving that the single sequence assumption was not appropriate for helix-coil transition. Conformational sampling has been a long-standing issue in computational sciences. In the third study, we systematically tested the convergence of the Replica Exchange Molecular Dynamics method (REMD), which is a recently developed method for conformational sampling enhancement. The results suggested that REMD can significantly enhance the sampling efficiency and accurately reproduce the long-time MD results with high efficiency. However, fluctuations at low temperatures (300 K) indicated that REMD simulations did not converge within our simulation time (14 ns). Much longer REMD simulation time might be needed for the system to reach thermodynamic equilibrium than expected. Finding the optimal side chain packing is a common issue in structure prediction, protein design and protein docking. In the fourth study, a new method was presented. The method overcame the rough energy landscape problem and enabled all-atom MD simulation to be applied directly to protein structure refinement. The method showed very successful results on buried side-chain assignments, nearly 100% accuracy on all 6 randomly picked proteins was reached; the results also clearly demonstrated that the proposed method can significantly enhance conformational sampling. These encouraging results suggested prospective applications on many other protein related systems.
Author : Lakhmi C. Jain
Publisher : Springer
ISBN 13 : 8132222024
Total Pages : 716 pages
Book Rating : 4.1/5 (322 download)
Download or read book Computational Intelligence in Data Mining - Volume 3 written by Lakhmi C. Jain and published by Springer. This book was released on 2014-12-11 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: The contributed volume aims to explicate and address the difficulties and challenges for the seamless integration of two core disciplines of computer science, i.e., computational intelligence and data mining. Data Mining aims at the automatic discovery of underlying non-trivial knowledge from datasets by applying intelligent analysis techniques. The interest in this research area has experienced a considerable growth in the last years due to two key factors: (a) knowledge hidden in organizations’ databases can be exploited to improve strategic and managerial decision-making; (b) the large volume of data managed by organizations makes it impossible to carry out a manual analysis. The book addresses different methods and techniques of integration for enhancing the overall goal of data mining. The book helps to disseminate the knowledge about some innovative, active research directions in the field of data mining, machine and computational intelligence, along with some current issues and applications of related topics.
Author : Shin Sedai Konpyūta Gijutsu Kaihatsu Kikō (Japan)
Publisher :
ISBN 13 :
Total Pages : 10 pages
Book Rating : 4.:/5 (123 download)
Download or read book A Three-dimensional Animation System for Protein Folding Simulation written by Shin Sedai Konpyūta Gijutsu Kaihatsu Kikō (Japan) and published by . This book was released on 1993 with total page 10 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : David M. Ferguson
Publisher : John Wiley & Sons
ISBN 13 : 0470142170
Total Pages : 576 pages
Book Rating : 4.4/5 (71 download)
Download or read book Monte Carlo Methods in Chemical Physics written by David M. Ferguson and published by John Wiley & Sons. This book was released on 2009-09-09 with total page 576 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Monte Carlo Methods in Chemical Physics: An Introduction to the Monte Carlo Method for Particle Simulations J. Ilja Siepmann Random Number Generators for Parallel Applications Ashok Srinivasan, David M. Ceperley and Michael Mascagni Between Classical and Quantum Monte Carlo Methods: "Variational" QMC Dario Bressanini and Peter J. Reynolds Monte Carlo Eigenvalue Methods in Quantum Mechanics and Statistical Mechanics M. P. Nightingale and C.J. Umrigar Adaptive Path-Integral Monte Carlo Methods for Accurate Computation of Molecular Thermodynamic Properties Robert Q. Topper Monte Carlo Sampling for Classical Trajectory Simulations Gilles H. Peslherbe Haobin Wang and William L. Hase Monte Carlo Approaches to the Protein Folding Problem Jeffrey Skolnick and Andrzej Kolinski Entropy Sampling Monte Carlo for Polypeptides and Proteins Harold A. Scheraga and Minh-Hong Hao Macrostate Dissection of Thermodynamic Monte Carlo Integrals Bruce W. Church, Alex Ulitsky, and David Shalloway Simulated Annealing-Optimal Histogram Methods David M. Ferguson and David G. Garrett Monte Carlo Methods for Polymeric Systems Juan J. de Pablo and Fernando A. Escobedo Thermodynamic-Scaling Methods in Monte Carlo and Their Application to Phase Equilibria John Valleau Semigrand Canonical Monte Carlo Simulation: Integration Along Coexistence Lines David A. Kofke Monte Carlo Methods for Simulating Phase Equilibria of Complex Fluids J. Ilja Siepmann Reactive Canonical Monte Carlo J. Karl Johnson New Monte Carlo Algorithms for Classical Spin Systems G. T. Barkema and M.E.J. Newman
Author : 林約丞
Publisher :
ISBN 13 :
Total Pages : 86 pages
Book Rating : 4.:/5 (71 download)
Download or read book A New Branch and Bound Method for the Protein Folding Problem in the 3D HP Model written by 林約丞 and published by . This book was released on 2010 with total page 86 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Leonidas Kapsokalyvas
Publisher :
ISBN 13 :
Total Pages : 340 pages
Book Rating : 4.:/5 (757 download)
Download or read book Local Search-based Protein Folding Simulations written by Leonidas Kapsokalyvas and published by . This book was released on 2011 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract. Protein folding is the physical process in which a protein acquires its structure that allows it to perform a specific biological task. Proteins fold spon-taneously into three-dimensional structures of minimum energy when found in the appropriate environment. The study of this phenomenon is often facilitated through local search-based computer simulations in which the energy of a protein is mini¬mized. This thesis is concerned with local search methods for protein folding simulations in rectangular and triangular lattice models as well as in a simplified coarse-grained off-lattice model. The aim of those simulations is on the one hand protein struc¬ture prediction and on the other hand energy landscape analysis. Lattice models are often useful in the study of protein folding, since they allow exact enumeration of solutions, easy identification of local minima and paths leading to them. The challenge for local search-based methods in lattice model simulations is to efficiently sample an exponentially large search space. In that respect this thesis contributes a method to reduce the search space in rectangular lattices, which is adapted into specific neighborhood relations and is used in local search methods. This method is based on restricting search to a reduced subspace of protein structures, free from some special symmetrical versions of the same structure. The thesis also contributes a novel local search method for protein structure prediction, namely a population based local search. The novel local search method can be used to gather local min¬ima of the underlying energy landscape. The method outperforms the state-of-the-art method tested for the specific set of benchmarks in the cubic lattice and the MJ(Miyazawa-Jernigan) energy model. The survey of the energy landscape in the latter model reveals that the energy of local minima follows a Gaussian-like distri¬bution.
Author : Garegin A. Papoian
Publisher : CRC Press
ISBN 13 : 1466576170
Total Pages : 430 pages
Book Rating : 4.4/5 (665 download)
Download or read book Coarse-Grained Modeling of Biomolecules written by Garegin A. Papoian and published by CRC Press. This book was released on 2017-10-30 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt: "The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.
Author :
Publisher :
ISBN 13 :
Total Pages : 866 pages
Book Rating : 4.3/5 (91 download)
Download or read book Biomedical Index to PHS-supported Research written by and published by . This book was released on 1990 with total page 866 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Maria Fyta
Publisher : Morgan & Claypool Publishers
ISBN 13 : 168174418X
Total Pages : 166 pages
Book Rating : 4.6/5 (817 download)
Download or read book Computational Approaches in Physics written by Maria Fyta and published by Morgan & Claypool Publishers. This book was released on 2016-11-01 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Approaches in Physics reviews computational schemes which are used in the simulations of physical systems. These range from very accurate ab initio techniques up to coarse-grained and mesoscopic schemes. The choice of the method is based on the desired accuracy and computational efficiency. A bottom-up approach is used to present the various simulation methods used in Physics, starting from the lower level and the most accurate methods, up to particle-based ones. The book outlines the basic theory underlying each technique and its complexity, addresses the computational implications and issues in the implementation, as well as present representative examples. A link to the most common computational codes, commercial or open source is listed in each chapter. The strengths and deficiencies of the variety of techniques discussed in this book are presented in detail and visualization tools commonly used to make the simulation data more comprehensive are also discussed. In the end, specific techniques are used as bridges across different disciplines. To this end, examples of different systems tackled with the same methods are presented. The appendices include elements of physical theory which are prerequisites in understanding the simulation methods.
Author : Tamar Schlick
Publisher : Springer Science & Business Media
ISBN 13 : 0387224645
Total Pages : 669 pages
Book Rating : 4.3/5 (872 download)
Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text
