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Computational Approaches To Protein Dynamics

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Computational Approaches To Protein Dynamics

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Author : Monika Fuxreiter
language : en
Publisher: CRC Press
Release Date : 2014-12-24

Computational Approaches To Protein Dynamics written by Monika Fuxreiter and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2014-12-24 with Science categories.

Computational Approaches To Protein Dynamics

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Author : Monika Fuxreiter
language : en
Publisher: CRC Press
Release Date : 2015-01-08

The Latest Developments on the Role of Dynamics in Protein Functions Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, and biology show how these advanced methods provide insights into dynamic aspects of biochemical processes. A particular focus is on intrinsically disordered proteins (IDPs), which lack a well-defined three-dimensional structure and function as dynamic ensembles. The book covers a wide spectrum of dynamics, from electronic structure-based to coarse-grained techniques via multiscaling at different levels. After an introduction to dynamics and historical overview of basic methodologies, the book addresses the following issues: Is there a quantitative relationship between enzymatic catalysis and protein dynamics? Which are the functionally relevant motions of proteins? How can structural properties and partner recognition mechanisms of IDPs be simulated? How can we speed up molecular dynamics? How can we describe conformational ensembles by the synergistic effort of computations and experiments? While dynamics is now considered essential for interpreting protein action, it is not yet an integral component in establishing structure–function relationships of proteins. Helping to reshape this classical view in biochemistry, this groundbreaking book explores advances in computational methodology and contributes to the new, ensemble way of studying proteins.

Computational Molecular Dynamics Challenges Methods Ideas

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Author : Peter Deuflhard
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-12-06

Computational Molecular Dynamics Challenges Methods Ideas written by Peter Deuflhard 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 2012-12-06 with Mathematics categories.

On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

Computational Approaches For Protein Dynamics And Function

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Author : Robert Jernigan
language : en
Publisher:
Release Date : 2024-11-11

Computational Approaches For Protein Dynamics And Function written by Robert Jernigan and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-11-11 with Science categories.

Proteins are fascinating structures that operate at the nanoscale in a complex environment and are involved in an astonishingly wide variety of functions, from ion transport to enzymatic catalysis, metabolism, neurotransmission, and many more functions. Understanding these peculiar functionalities at the single-protein level requires advanced experimental and computational techniques. In the era of high-performance computing, computational methods are particularly well suited to investigating the structure and dynamics of proteins and unravelling how they enable biological functions. Molecular Dynamics (MD), Normal Mode Analysis (NMA), and Elastic Network Models (ENMs) are just a few examples of the computational methodologies that we can use to elucidate protein conformational dynamics, allostery, the impact of mutations, and many other fascinating subjects. This Special Issue comprises eight peer-reviewed papers demonstrating how various computational approaches can be employed to address the ultimate and most crucial question: how do proteins work?

From Protein Structure To Function With Bioinformatics

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Author : Daniel John Rigden
language : en
Publisher: Springer Science & Business Media
Release Date : 2008-12-11

From Protein Structure To Function With Bioinformatics written by Daniel John Rigden 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 2008-12-11 with Science categories.

Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.

Computational Protein Design

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Author : Ilan Samish
language : en
Publisher: Humana
Release Date : 2016-12-03

Computational Protein Design written by Ilan Samish and has been published by Humana this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-12-03 with Science categories.

The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.

Killer Cell Dynamics

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Author : Dominik Wodarz
language : en
Publisher: Springer Science & Business Media
Release Date : 2007-04-05

Killer Cell Dynamics written by Dominik Wodarz 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 2007-04-05 with Mathematics categories.

Systems biology and computational biology have recently become prominent areas of research in the biomedical community, especially in the area of cell biology. Given that much information on genes and their protein products has become available, the big question is how the individual components interact and work together, and how this determines the functioning of cells, organs, and organisms. Long before the popularity of systems biology in biomedicine, however, such approaches have been used successfully in a di?erent area of biology: population ecology. Research in the area of population dynamics - vestigated complex interactions between di?erent populations of organisms, such as the dynamics of competition and predation, food webs, community structure, as well as the epidemiology of infectious diseases. In this ?eld, t- oretical biology and mathematical modeling have become an integral part of research. Mathematical models allowed people to obtain interesting and counter-intuitive insights into how complex interactions among di?erent p- ulations can play out. Such mathematical studies not only gave rise to - teresting theoretical ideas, but also provided the basis for the design of new experimental work and de?ned major questions and directions of research. Around 1990, such population dynamic concepts, and the use of mathema- cal/computational approaches, started to be applied to the in vivo dynamics between viruses and the immune system. These interactions have many s- ilarities to ecological, epidemiological, and evolutionary principles. Consider theepidemiologicalspreadofapathogen(suchasthecommoncold)througha population of hosts.

Computational Approaches For Studying Enzyme Mechanism Part B

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Author :
language : en
Publisher: Academic Press
Release Date : 2016-08-03

Computational Approaches For Studying Enzyme Mechanism Part B written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-08-03 with Science categories.

Computational Approaches for Studying Enzyme Mechanism, Part B is the first of two volumes in the Methods in Enzymology series that focuses on computational approaches for studying enzyme mechanism. The serial achieves the critically acclaimed gold standard of laboratory practices and remains one of the most highly respected publications in the molecular biosciences. Each volume is eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with over 550 volumes, the series remains a prominent and essential publication for researchers in all fields of the life sciences and biotechnology, including biochemistry, chemical biology, microbiology, synthetic biology, cancer research, genetics, and other fields of study. - Focuses on computational approaches for studying enzyme mechanism - Continues the legacy of this premier serial with quality chapters authored by leaders in the field - Covers research methods in intermediate filament associated proteins, and contains sections on such topics as lamin-associated proteins, intermediate filament-associated proteins and plakin, and other cytoskeletal cross-linkers

Computational Structural Biology

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Author : Manuel Claude Peitsch
language : en
Publisher: World Scientific
Release Date : 2008

Computational Structural Biology written by Manuel Claude Peitsch and has been published by World Scientific this book supported file pdf, txt, epub, kindle and other format this book has been release on 2008 with Science categories.

This work covers the impact of computational structural biology on protein structure prediction methods, macromolecular function and protein design, and key methods in drug discovery. It also addresses the computational challenges of experimental approaches in structural biology.

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.

Computational Approaches To Protein Dynamics

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