Computational Methods For Protein Modeling And Design Based On An Ensemble View Of Protein Structures
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Computational Methods For Protein Modeling And Design Based On An Ensemble View Of Protein Structures
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Author : Fan Zheng
language : en
Publisher:
Release Date : 2016
Computational Methods For Protein Modeling And Design Based On An Ensemble View Of Protein Structures written by Fan Zheng and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016 with categories.
Understanding sequence-structure relationships of proteins is a central theme of computational structural biology. To create accurate mapping between sequences and structures is a big computational challenge, because the inherent dynamics of protein molecules requires any structure to be seen as an ensemble containing a large number of structural states. In this thesis, I focus on developing new structural modeling methods representing two routes towards efficient sequence-structure mapping that are compatible with this ensemble view of structures. First, I will show that the relationships between the sequence and the structural ensemble of a protein can be revealed by breaking down the protein into constituent structural fragments, for which ensemble statistics can be obtained from the protein structure database. Second, sequence-structure relationships can be also extracted by combining explicit atomistic modeling of ensembles and statistical tools reducing the overall computational cost. Implications in structure prediction, mutational analysis, and design of protein-interaction modulators will be presented and discussed, showing the great promise held by these methods in further improving the state-of-the-art in a broad spectrum of applications in computational structural biology.
Computational Methods For Protein Structure Prediction And Modeling
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Author : Ying Xu
language : en
Publisher: Springer Science & Business Media
Release Date : 2010-05-05
Computational Methods For Protein Structure Prediction And Modeling written by Ying Xu 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 2010-05-05 with Science categories.
Volume Two of this two-volume sequence presents a comprehensive overview of protein structure prediction methods and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics.
Computational Methods For Protein Structure Prediction And Modeling
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Author : Ying Xu
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-08-24
Computational Methods For Protein Structure Prediction And Modeling written by Ying Xu 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 2007-08-24 with Science categories.
Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.
Computational Methods For Protein Structure Prediction And Modeling
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Author : Ying Xu
language : en
Publisher: Springer
Release Date : 2010-12-01
Computational Methods For Protein Structure Prediction And Modeling written by Ying Xu and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-12-01 with Science categories.
Volume Two of this two-volume sequence presents a comprehensive overview of protein structure prediction methods and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics.
Introduction To Protein Structure Prediction
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Author : Huzefa Rangwala
language : en
Publisher: John Wiley & Sons
Release Date : 2011-03-16
Introduction To Protein Structure Prediction written by Huzefa Rangwala and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-03-16 with Science categories.
A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.
Protein Modelling
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Author : Andrew Gamble
language : en
Publisher: Springer
Release Date : 2014-11-13
Protein Modelling written by Andrew Gamble and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-11-13 with Science categories.
In this volume, a detailed description of cutting-edge computational methods applied to protein modeling as well as specific applications are presented. Chapters include: the application of Car-Parrinello techniques to enzyme mechanisms, the outline and application of QM/MM methods, polarizable force fields, recent methods of ligand docking, molecular dynamics related to NMR spectroscopy, computer optimization of absorption, distribution, metabolism and excretion extended by toxicity for drugs, enzyme design and bioinformatics applied to protein structure prediction. A keen emphasis is laid on the clear presentation of complex concepts, since the book is primarily aimed at Ph.D. students, who need an insight in up-to-date protein modeling. The inclusion of descriptive, color figures will allow the reader to get a pictorial representation of complicated structural issues.
Protein Structure Prediction A Practical Approach
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Author : Michael J. E. Sternberg
language : en
Publisher: Oxford University Press, USA
Release Date : 1996-11-28
Protein Structure Prediction A Practical Approach written by Michael J. E. Sternberg and has been published by Oxford University Press, USA this book supported file pdf, txt, epub, kindle and other format this book has been release on 1996-11-28 with categories.
The three-dimensional structure of proteins is a key factor in their biological activity. There is an increasing need to be able to predict the structure of a protein once its amino-acid sequence is known; this book presents practical methods of achieving that ambitious aim, using the latest computer modelling algorithms. - ;The prediction of the three-dimensional structure of a protein from its sequence is a problem faced by an ever-increasing number of biological scientists as they strive to utilize genetic information. The increasing sizes of the sequence and structural databases, the improvements in computing power, and the deeper understanding of the principles of protein structure have led to major developments in the field in the last few years. This book presents practical computer-based methods using the latest computer modelling algorithms. -
Computational Methods For Protein Structure Prediction And Modeling Basic Characterization
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Author :
language : en
Publisher:
Release Date : 2007
Computational Methods For Protein Structure Prediction And Modeling Basic Characterization written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Computational biology categories.
Protein Structure Prediction
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Author : Mohammed Zaki
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-09-12
Protein Structure Prediction written by Mohammed Zaki 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 2007-09-12 with Science categories.
This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.
Computational Methods For Protein Structure Prediction And Modeling Structure Prediction
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Author :
language : en
Publisher:
Release Date : 2007
Computational Methods For Protein Structure Prediction And Modeling Structure Prediction written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Computational biology categories.