Computer Simulations Of Protein Folding
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Computer Simulations Of Protein Folding
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Author : Atipat Rojnuckarin
language : en
Publisher:
Release Date : 1998
Computer Simulations Of Protein Folding written by Atipat Rojnuckarin and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1998 with categories.
Computer Simulations Of Protein Structures And Interactions
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Author : Serafin Fraga
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-04-17
Computer Simulations Of Protein Structures And Interactions written by Serafin Fraga and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-04-17 with Science categories.
Protein engineering endeavors to design new peptides and proteins or to change the structural and/or functional characteristics of existing ones for specific purposes, opening the way for the development of new drugs. This work develops in a comprehensive way the theoretical formulation for the methods used in computer-assisted modeling and predictions, starting from the basic concepts and proceeding to the more sophisticated methods, such as Monte Carlo and molecular dynamics. An evaluation of the approximations inherent to the simulations will allow the reader to obtain a perspective of the possible deficiencies and difficulties and approach the task with realistic expectations. Examples from the authors laboratories, as well as from the literature provide useful information.
Computer Simulations Of Protein Folding
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Author : Haydn Wyn Williams
language : en
Publisher:
Release Date : 2011
Computer Simulations Of Protein Folding written by Haydn Wyn Williams and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011 with categories.
Computer simulations of biological systems provide novel data while both supporting and challenging traditional experimental methods. However, continued innovation is required to ensure that these technologies are able to work with increasingly complex systems. Coarse-grained approximations of protein structure have been studied using a lattice model designed to find low-energy conformations. A hydrogen-bonding term has been introduced. The ability to form [beta]-sheet has been demonstrated, and the intricacies of reproducing the more complex [alpha]-helix on a lattice have been considered. An alternative strategy, that of better utilising computing power through the technique of milestoning, has shown good agreement with previous experimental and computational work. The increased efficiency allows significantly less extreme simulation conditions to be applied than those used in alternative simulation methods, and allows more simulation repeats. Finally, the principles of Least Action Dynamics have been employed to combine the two approaches described above. By splitting a simulation trajectory into a number of smaller components, and using the lattice model to optimise the path from a start structure to an end structure, it has been possible to efficiently generate dynamical information using an alternative method to traditional molecular dynamics.
Computer Simulations Of Protein Folding And Aggregation
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Author : Hung Duc Nguyen
language : en
Publisher:
Release Date : 2004
Computer Simulations Of Protein Folding And Aggregation written by Hung Duc Nguyen and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with categories.
Keywords: fibril formation, protein folding, protein aggregation, polyalanine, amyloid, computer simulation, molecular dynamics.
Protein Folding
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Author : C. M. Dobson
language : en
Publisher: Cambridge University Press
Release Date : 1995
Protein Folding written by C. M. Dobson and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 1995 with Medical categories.
Discusses the molecular mechanisms controlling protein folding in vivo and in vitro.
Protein Folding Misfolding And Aggregation
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Author : Victor Muñoz
language : en
Publisher: Royal Society of Chemistry
Release Date : 2008-06-24
Protein Folding Misfolding And Aggregation written by Victor Muñoz and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008-06-24 with Science categories.
Protein folding and aggregation is the process by which newly synthesized proteins fold into the specific three-dimensional structures defining their biologically active states. It has always been a major focus of research in biochemistry and has often been seen as the unsolved second part of the genetic code. In the last 10 years we have witnessed a quantum leap in the research in this exciting area. Computational methods have improved to the extent of making possible to simulate the complete folding process of small proteins and the early stages of protein aggregation. Experimental methods have evolved to permit resolving fast processes of folding reactions and visualizing single molecules during folding. The findings from these novel experiments and detailed computer simulations have confirmed the main predictions of analytical theory of protein folding. In summary, protein folding research has finally acquired the status of a truly quantitative science, paving the way for more exciting developments in the near future. This unique book covers all the modern approaches and the many advances experienced in the field during the last 10 years. There is also much emphasis on computational methods and studies of protein aggregation which have really flourished in the last decade. It includes chapters in the areas that have witnessed major developments and are written by top experts including:computer simulations of folding, fast folding, single molecule spectroscopy, protein design, aggregation studies (both computational and experimental). Readers will obtain a unique perspective of the problems faced in the biophysical study of protein conformational behaviour in aqueous solution and how these problems are being solved with a multidisciplinary approach that combines theory, experiment and computer simulations. Protein Folding, Misfolding and Aggregation Classical Themes and Novel Approaches is essential reading for graduate students actively involved in protein folding research, other scientists interested in the recent progress of the field and instructors revamping the protein folding section of their biochemistry and biophysics courses.
Computer Simulations Of Protein Folding And Aggregation
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Author :
language : en
Publisher:
Release Date : 2004
Computer Simulations Of Protein Folding And Aggregation written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with categories.
Computer simulation is used to study the competition between protein folding and aggregation, especially the formation of ordered structures that are also known as amyloid fibrils. Employing simplified protein models, we simulate multi-protein systems at a greater level of detail than has previously been possible, probe the fundamental physics that govern protein folding and aggregation, and explore the energetic and structural characteristics of amorphous and fibrillar protein aggregates. We first tackle the aggregation problem by using a low-resolution model called the lattice HP model developed by Lau and Dill. Dynamic Monte Carlo simulations are conducted on a system of simple, two-dimensional lattice protein molecules. We investigate how changing the rate of chemical or thermal renaturation affects the folding and aggregation behavior of the model protein molecule by simulating three renaturation methods: infinitely slow cooling, slow but finite cooling, and quenching. We find that the infinitely slow cooling method provides the highest refolding yields. We then study how the variation of protein concentration affects the refolding yield by simulating the pulse renaturation method, in which denatured proteins are slowly added to the refolding simulation box in a stepwise manner. We observe that the pulse renaturation method provides refolding yields that are substantially higher than those observed in the other three methods even at high packing fractions. We then investigate the folding of a polyalanine peptide with the sequence Ac-KA14K-NH2 using a novel off-lattice, intermediate-resolution protein model originally developed by Smith and Hall. The thermodynamics of a system containing a single Ac-KA14K-NH2 molecule is explored by employing the replica exchange simulation method to map out the conformational transitions as a function of temperature. We also explore the influence of solvent type on the folding process by varying the relative strength of the sid.
Computer Simulations In Condensed Matter From Materials To Chemical Biology Volume 2
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Author : Mauro Ferrario
language : en
Publisher: Springer
Release Date : 2007-04-16
Computer Simulations In Condensed Matter From Materials To Chemical Biology Volume 2 written by Mauro Ferrario and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-04-16 with Science categories.
This extensive and comprehensive collection of lectures by world-leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 2 offers surveys on numerical experiments carried out for a great number of systems, ranging from materials sciences to chemical biology, including supercooled liquids, spin glasses, colloids, polymers, liquid crystals, biological membranes and folding proteins.
Computer Simulation Of Liquids
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Author : Michael P. Allen
language : en
Publisher: Oxford University Press
Release Date : 2017-08-15
Computer Simulation Of Liquids written by Michael P. Allen and has been published by Oxford University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-08-15 with Science categories.
This book provides a practical guide to molecular dynamics and Monte Carlo simulation techniques used in the modelling of simple and complex liquids. Computer simulation is an essential tool in studying the chemistry and physics of condensed matter, complementing and reinforcing both experiment and theory. Simulations provide detailed information about structure and dynamics, essential to understand the many fluid systems that play a key role in our daily lives: polymers, gels, colloidal suspensions, liquid crystals, biological membranes, and glasses. The second edition of this pioneering book aims to explain how simulation programs work, how to use them, and how to interpret the results, with examples of the latest research in this rapidly evolving field. Accompanying programs in Fortran and Python provide practical, hands-on, illustrations of the ideas in the text.
Protein Folding Dynamics And Stability
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Author : Prakash Saudagar
language : en
Publisher: Springer Nature
Release Date : 2023-05-27
Protein Folding Dynamics And Stability written by Prakash Saudagar and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-05-27 with Science categories.
This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.