Markov State Models For Protein And Rna Folding
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Markov State Models For Protein And Rna Folding
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Author : Gregory Ross Bowman
language : en
Publisher: Stanford University
Release Date : 2010
Markov State Models For Protein And Rna Folding written by Gregory Ross Bowman and has been published by Stanford University this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Understanding the molecular bases of human health could greatly augment our ability to prevent and treat diseases. For example, a deeper understanding of protein folding would serve as a reference point for understanding, preventing, and reversing protein misfolding in diseases like Alzheimer's. Unfortunately, the small size and tremendous flexibility of proteins and other biomolecules make it difficult to simultaneously monitor their thermodynamics and kinetics with sufficient chemical detail. Atomistic Molecular Dynamics (MD) simulations can provide a solution to this problem in some cases; however, they are often too short to capture biologically relevant timescales with sufficient statistical accuracy. We have developed a number of methods to address these limitations. In particular, our work on Markov State Models (MSMs) now makes it possible to map out the conformational space of biomolecules by combining many short simulations into a single statistical model. Here we describe our use of MSMs to better understand protein and RNA folding. We chose to focus on these folding problems because of their relevance to misfolding diseases and the fact that any method capable of describing such drastic conformational changes should also be applicable to less dramatic but equally important structural rearrangements like allostery. One of the key insights from our folding simulations is that protein native states are kinetic hubs. That is, the unfolded ensemble is not one rapidly mixing set of conformations. Instead, there are many non-native states that can each interconvert more rapidly with the native state than with one another. In addition to these general observations, we also demonstrate how MSMs can be used to make predictions about the structural and kinetic properties of specific systems. Finally, we explain how MSMs and other enhanced sampling algorithms can be used to drive efficient sampling.
Markov State Models For Protein And Rna Folding
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Author : Gregory Ross Bowman
language : en
Publisher:
Release Date : 2010
Markov State Models For Protein And Rna Folding written by Gregory Ross Bowman and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Understanding the molecular bases of human health could greatly augment our ability to prevent and treat diseases. For example, a deeper understanding of protein folding would serve as a reference point for understanding, preventing, and reversing protein misfolding in diseases like Alzheimer's. Unfortunately, the small size and tremendous flexibility of proteins and other biomolecules make it difficult to simultaneously monitor their thermodynamics and kinetics with sufficient chemical detail. Atomistic Molecular Dynamics (MD) simulations can provide a solution to this problem in some cases; however, they are often too short to capture biologically relevant timescales with sufficient statistical accuracy. We have developed a number of methods to address these limitations. In particular, our work on Markov State Models (MSMs) now makes it possible to map out the conformational space of biomolecules by combining many short simulations into a single statistical model. Here we describe our use of MSMs to better understand protein and RNA folding. We chose to focus on these folding problems because of their relevance to misfolding diseases and the fact that any method capable of describing such drastic conformational changes should also be applicable to less dramatic but equally important structural rearrangements like allostery. One of the key insights from our folding simulations is that protein native states are kinetic hubs. That is, the unfolded ensemble is not one rapidly mixing set of conformations. Instead, there are many non-native states that can each interconvert more rapidly with the native state than with one another. In addition to these general observations, we also demonstrate how MSMs can be used to make predictions about the structural and kinetic properties of specific systems. Finally, we explain how MSMs and other enhanced sampling algorithms can be used to drive efficient sampling.
An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation
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Author : Gregory R. Bowman
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-12-02
An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation written by Gregory R. Bowman 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 2013-12-02 with Science categories.
The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
Metastability And Markov State Models In Molecular Dynamics
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Author : Christof Schütte
language : en
Publisher: American Mathematical Soc.
Release Date : 2013-12-26
Metastability And Markov State Models In Molecular Dynamics written by Christof Schütte and has been published by American Mathematical Soc. this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-12-26 with Mathematics categories.
Applications in modern biotechnology and molecular medicine often require simulation of biomolecular systems in atomic representation with immense length and timescales that are far beyond the capacity of computer power currently available. As a consequence, there is an increasing need for reduced models that describe the relevant dynamical properties while at the same time being less complex. In this book the authors exploit the existence of metastable sets for constructing such a reduced molecular dynamics model, the so-called Markov state model (MSM), with good approximation properties on the long timescales. With its many examples and illustrations, this book is addressed to graduate students, mathematicians, and practical computational scientists wanting an overview of the mathematical background for the ever-increasing research activity on how to construct MSMs for very different molecular systems ranging from peptides to proteins, from RNA to DNA, and via molecular sensors to molecular aggregation. This book bridges the gap between mathematical research on molecular dynamics and its practical use for realistic molecular systems by providing readers with tools for performing in-depth analysis of simulation and data-analysis methods. Titles in this series are co-published with the Courant Institute of Mathematical Sciences at New York University.
Artificial Chemistries
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Author : Wolfgang Banzhaf
language : en
Publisher: MIT Press
Release Date : 2024-03-19
Artificial Chemistries written by Wolfgang Banzhaf and has been published by MIT Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-03-19 with Science categories.
An introduction to the fundamental concepts of the emerging field of Artificial Chemistries, covering both theory and practical applications. The field of Artificial Life (ALife) is now firmly established in the scientific world, but it has yet to achieve one of its original goals: an understanding of the emergence of life on Earth. The new field of Artificial Chemistries draws from chemistry, biology, computer science, mathematics, and other disciplines to work toward that goal. For if, as it has been argued, life emerged from primitive, prebiotic forms of self-organization, then studying models of chemical reaction systems could bring ALife closer to understanding the origins of life. In Artificial Chemistries (ACs), the emphasis is on creating new interactions rather than new materials. The results can be found both in the virtual world, in certain multiagent systems, and in the physical world, in new (artificial) reaction systems. This book offers an introduction to the fundamental concepts of ACs, covering both theory and practical applications. After a general overview of the field and its methodology, the book reviews important aspects of biology, including basic mechanisms of evolution; discusses examples of ACs drawn from the literature; considers fundamental questions of how order can emerge, emphasizing the concept of chemical organization (a closed and self-maintaining set of chemicals); and surveys a range of applications, which include computing, systems modeling in biology, and synthetic life. An appendix provides a Python toolkit for implementing ACs.
Pacific Symposium On Biocomputing 2010 Kamuela Hawaii Usa 4 8 January 2010
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Author : Russ B. Altman
language : en
Publisher: World Scientific
Release Date : 2009-10-23
Pacific Symposium On Biocomputing 2010 Kamuela Hawaii Usa 4 8 January 2010 written by Russ B. Altman and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-10-23 with Mathematics categories.
The Pacific Symposium on Biocomputing (PSB) 2010 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2010 will be held on January 4 - 8, 2010 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference. PSB 2010 will bring together top researchers from the US, Asia Pacific, and around the world to exchange research results and address pertinent issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology. The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's "hot topics". In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.
Biocomputing 2010 Proceedings Of The Pacific Symposium
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Author : Russ B Altman
language : en
Publisher: World Scientific
Release Date : 2009-10-23
Biocomputing 2010 Proceedings Of The Pacific Symposium written by Russ B Altman and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-10-23 with Mathematics categories.
The Pacific Symposium on Biocomputing (PSB) 2010 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2010 will be held on January 4 - 8, 2010 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2010 will bring together top researchers from the US, Asia Pacific, and around the world to exchange research results and address pertinent issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's “hot topics”. In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.
Protein Conformational Dynamics
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Author : Ke-li Han
language : en
Publisher: Springer Science & Business Media
Release Date : 2014-01-20
Protein Conformational Dynamics written by Ke-li Han 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 2014-01-20 with Medical categories.
This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
From Computational Biophysics To Systems Biology Cbsb11 Celebrating Harold Scheraga S 90th Birthday
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Author : Paolo Carloni
language : en
Publisher: Forschungszentrum Jülich
Release Date : 2012
From Computational Biophysics To Systems Biology Cbsb11 Celebrating Harold Scheraga S 90th Birthday written by Paolo Carloni and has been published by Forschungszentrum Jülich this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with categories.
Intelligent Computing Theories And Application
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Author : De-Shuang Huang
language : en
Publisher: Springer
Release Date : 2018-08-08
Intelligent Computing Theories And Application written by De-Shuang Huang and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-08-08 with Computers categories.
This two-volume set LNCS 10954 and LNCS 10955 constitutes - in conjunction with the volume LNAI 10956 - the refereed proceedings of the 14th International Conference on Intelligent Computing, ICIC 2018, held in Wuhan, China, in August 2018. The 275 full papers and 72 short papers of the three proceedings volumes were carefully reviewed and selected from 632 submissions. The papers are organized in topical sections such as Neural Networks.- Pattern Recognition.- Image Processing.- Intelligent Computing in Robotics.- Intelligent Control and Automation.- Intelligent Data Analysis and Prediction.- Fuzzy Theory and Algorithms.- Supervised Learning.- Unsupervised Learning.- Kernel Methods and Supporting Vector Machines.- Knowledge Discovery and Data Mining.- Natural Language Processing and Computational Linguistics.- Gene Expression Array Analysis.- Systems Biology.- Computational Genomics.- Computational Proteomics.- Gene Regulation Modeling and Analysis.- Protein-Protein Interaction Prediction.- Next-Gen Sequencing and Metagenomics.- Structure Prediction and Folding.- Evolutionary Optimization for Scheduling.- High-Throughput Biomedical Data Integration and Mining.- Machine Learning Algorithms and Applications.- Heuristic Optimization Algorithms for Real-World Applications.- Evolutionary Multi-Objective Optimization and Its Applications.- Swarm Evolutionary Algorithms for Scheduling and Combinatorial.- Optimization.- Swarm Intelligence and Applications in Combinatorial Optimization.- Advances in Metaheuristic Optimization Algorithm.- Advances in Image Processing and Pattern Recognition Techniques.- AI in Biomedicine.- Bioinformatics.- Biometrics Recognition.- Information Security.- Virtual Reality and Human-Computer Interaction.- Healthcare Informatics Theory and Methods.- Intelligent Computing in Computer Vision.- Intelligent Agent and Web Applications.- Reinforcement Learning.- Machine Learning.- Modeling, Simulation, and Optimization of Biological Systems.- Biomedical Data Modeling and Mining.- Cheminformatics.- Intelligent Computing in Computational Biology.- Protein Structure and Function Prediction.- Biomarker Discovery.- Hybrid Computational Intelligence: Theory and Application in Bioinformatics, Computational Biology and Systems Biology.- IoT and Smart Data.- Intelligent Systems and Applications for Bioengineering.- Evolutionary Optimization: Foundations and Its Applications to Intelligent Data Analytics.- Protein and Gene Bioinformatics: Analysis, Algorithms and Applications.