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Protein Folding in Silico

Protein Folding in Silico
  • Author : Irena Roterman-Konieczna
  • Publisher :Unknown
  • Release Date :2012-10-04
  • Total pages :240
  • ISBN : 9781908818256
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Summary : 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

Systems Biology

Systems Biology
  • Author : Leszek Konieczny,Irena Roterman-Konieczna,Paweł Spólnik
  • Publisher :Unknown
  • Release Date :2013-10-01
  • Total pages :204
  • ISBN : 9783319013367
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Summary : The objective of this book is to present the strategies employed by living organisms on a molecular level and to help understand the basics of Systems Biology. Its content is organized in a way to meet the exponential growth in the volume of biological knowledge, and the need for a multidisciplinary approach in the practice of teaching modern biology. For this reason, the whole material is divided into five chapters, each devoted to a fundamental concept: Structure-Function, Energy, Information, Regulation and Interrelationships. The book describes generic mechanisms which occur in biology and promotes a simulation-based approach to the subject of Systems Biology. The use of basic knowledge as the background for presenting biological problems obligates the teachers to deal with generalized phenomena comprising the ever increasing volume of teaching materials. This book is intended for biologists and is informative for specialists in the areas of computer science, robotics and engineering.

Abridged Thermodynamic and Thermochemical Tables

Abridged Thermodynamic and Thermochemical Tables
  • Author : Frederick Douglas Hamblin
  • Publisher :Unknown
  • Release Date :1968
  • Total pages :73
  • ISBN : 9780081029817
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Summary : The phenomenon of amyloidosis has attracted the attention of numerous researchers for two main reasons: (1) it involves unexpected changes in protein conformation (without chemical intervention) and (2) has practical implications, such as elucidating the mechanisms which drive neurodegenerative diseases carries. In particular, understanding the process of amyloidosis is a fundamental prerequisite in the search for new, effective drugs and therapies targeting the key area of neurodegenerative diseases. The book proposes a model and a mechanism which explain protein misfolding. The concepts presented are based on a model originally intended to show how proteins attain their native conformations. The model is quantitative in nature and founded upon arguments derived from information theory. It facilitates prediction and simulation of the amyloid fibrillation process. It also identifies progressive changes which occur in native proteins, leading to the emergence of amyloid aggregations.

Identification of Ligand Binding Site and Protein-Protein Interaction Area

Identification of Ligand Binding Site and Protein-Protein Interaction Area
  • Author : Irena Roterman-Konieczna
  • Publisher :Unknown
  • Release Date :2012-10-19
  • Total pages :170
  • ISBN : 9789400752849
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Summary : This volume presents a review of the latest numerical techniques used to identify ligand binding and protein complexation sites. It should be noted that there are many other theoretical studies devoted to predicting the activity of specific proteins and that useful protein data can be found in numerous databases. The aim of advanced computational techniques is to identify the active sites in specific proteins and moreover to suggest a generalized mechanism by which such protein-ligand (or protein-protein) interactions can be effected. Developing such tools is not an easy task – it requires extensive expertise in the area of molecular biology as well as a firm grasp of numerical modeling methods. Thus, it is often viewed as a prime candidate for interdisciplinary research.

Advances in Protein Chemistry and Structural Biology

Advances in Protein Chemistry and Structural Biology
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2014-03-11
  • Total pages :488
  • ISBN : 9780128003732
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Summary : This eclectic volume features two major topics: applications of mass spectrometry in bioscience; and computational methods for analysis of protein structure and interactions with other macromolecules. Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series has been the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics. Describes advances in application of powerful techniques in a wide bioscience area Chapters are written by authorities in their field Targeted to a wide audience of researchers, specialists, and students The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables

Structure and Action of Molecular Chaperones

Structure and Action of Molecular Chaperones
  • Author : Lila M Gierasch,Arthur L Horwich,Christine Slingsby,Sue Wickner,David Agard
  • Publisher :Unknown
  • Release Date :2016-08-08
  • Total pages :229
  • ISBN : 9789814749343
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Summary : This unique volume reviews the beautiful architectures and varying mechanical actions of the set of specialized cellular proteins called molecular chaperones, which provide essential kinetic assistance to processes of protein folding and unfolding in the cell. Ranging from multisubunit ring-shaped chaperonin and Hsp100 machines that use their central cavities to bind and compartmentalize action on proteins, to machines that use other topologies of recognition — binding cellular proteins in an archway or at the surface of a "clamp" or at the surface of a globular assembly — the structures show us the ways and means the cell has devised to assist its major effectors, proteins, to reach and maintain their unique active forms, as well as, when required, to disrupt protein structure in order to remodel or degrade. Each type of chaperone is beautifully illustrated by X-ray and EM structure determinations at near- atomic level resolution and described by a leader in the study of the respective family. The beauty of what Mother Nature has devised to accomplish essential assisting actions for proteins in vivo is fully appreciable.

Practical Bioinformatics

Practical Bioinformatics
  • Author : Janusz M. Bujnicki
  • Publisher :Unknown
  • Release Date :2007-09-12
  • Total pages :265
  • ISBN : 9783540742685
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Summary : This book presents applications of bioinformatics tools that experimental research scientists use in "daily practice." Its interdisciplinary approach combines computational and experimental methods to solve scientific problems. The book begins with reviews of computational methods for protein sequence-structure-function analysis, followed by methods that use experimental data obtained in the laboratory to improve functional predictions.

Biomolecular Assembly in Silico Using Massively Parallel Simulations to Probe Protein and RNA Folding Dynamics

Biomolecular Assembly in Silico Using Massively Parallel Simulations to Probe Protein and RNA Folding Dynamics
  • Author : Eric J. Sorin
  • Publisher :Unknown
  • Release Date :2007
  • Total pages :348
  • ISBN : STANFORD:36105128072415
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Summary :

Oxidative Folding of Proteins

Oxidative Folding of Proteins
  • Author : Matthias J Feige
  • Publisher :Unknown
  • Release Date :2018-07-30
  • Total pages :430
  • ISBN : 9781782629900
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Summary : The formation of disulphide bonds is probably the most influential modification of proteins. These bonds are unique among post-translational modifications of proteins as they can covalently link cysteine residues far apart in the primary sequence of a protein. This has the potential to convey stability to otherwise marginally stable structures of proteins. However, the reactivity of cysteines comes at a price: the potential to form incorrect disulphide bonds, interfere with folding, or even cause aggregation. An elaborate set of cellular machinery exists to catalyze and guide this process: facilitating bond formation, inhibiting unwanted pairings and scrutinizing the outcomes. Only in recent years has it become clear how intimately connected this cellular machinery is with protein folding helpers, organellar redox balance and cellular homeostasis as a whole. This book comprehensively covers the basic principles of disulphide bond formation in proteins and describes the enzymes involved in the correct oxidative folding of cysteine-containing proteins. The biotechnological and pharmaceutical relevance of proteins, their variants and synthetic replicates is continuously increasing. Consequently this book is an invaluable resource for protein chemists involved in realted research and production.

Protein Physics

Protein Physics
  • Author : Alexei V. Finkelstein,Oleg Ptitsyn
  • Publisher :Unknown
  • Release Date :2016-06-22
  • Total pages :528
  • ISBN : 9780081012369
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Summary : Protein Physics: A Course of Lectures covers the most general problems of protein structure, folding and function. It describes key experimental facts and introduces concepts and theories, dealing with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states. The book systematically summarizes and presents the results of several decades of worldwide fundamental research on protein physics, structure, and folding, describing many physical models that help readers make estimates and predictions of physical processes that occur in proteins. New to this revised edition is the inclusion of novel information on amyloid aggregation, natively disordered proteins, protein folding in vivo, protein motors, misfolding, chameleon proteins, advances in protein engineering & design, and advances in the modeling of protein folding. Further, the book provides problems with solutions, many new and updated references, and physical and mathematical appendices. In addition, new figures (including stereo drawings, with a special appendix showing how to use them) are added, making this an ideal resource for graduate and advanced undergraduate students and researchers in academia in the fields of biophysics, physics, biochemistry, biologists, biotechnology, and chemistry. Fully revised and expanded new edition based on the latest research developments in protein physics Written by the world's top expert in the field Deals with fibrous, membrane, and water-soluble globular proteins, in both their native and denatured states Summarizes, in a systematic form, the results of several decades of worldwide fundamental research on protein physics and their structure and folding Examines experimental data on protein structure in the post-genome era

Protein Engineering Handbook

Protein Engineering Handbook
  • Author : Stefan Lutz,Uwe Theo Bornscheuer
  • Publisher :Unknown
  • Release Date :2012-07-31
  • Total pages :1015
  • ISBN : 9783527667017
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Summary : Unparalleled in size and scope, this new major reference integrates academic and industrial knowledge into a single resource, allowing for a unique overview of the entire field. Adopting a systematic and practice-oriented approach, and including a wide range of technical and methodological information, this highly accessible handbook is an invaluable 'toolbox' for any bioengineer. In two massive volumes, it covers the full spectrum of current concepts, methods and application areas.

Handbook of Neurochemistry and Molecular Neurobiology

Handbook of Neurochemistry and Molecular Neurobiology
  • Author : Moussa B.H. Youdim,Moussa Youdin,Abel Lajtha,Peter Riederer,Leontino Battistin,Sylvia A. Mandel
  • Publisher :Unknown
  • Release Date :2007-12-14
  • Total pages :432
  • ISBN : 9780387303444
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Summary :

Protein Folding in the Cell

Protein Folding in the Cell
  • Author : Anonim
  • Publisher :Unknown
  • Release Date :2002-02-20
  • Total pages :550
  • ISBN : 9780080522401
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Summary : This volume of Advances in Protein Chemistry provides a broad, yet deep look at the cellular components that assist protein folding in the cell. This area of research is relatively new--10 years ago these components were barely recognized, so this book is a particularly timely compilation of current information. Topics covered include a review of the structure and mechanism of the major chaperone components, prion formation in yeast, and the use of microarrays in studying stress response. Outlines preceding each chapter allow the reader to quickly access the subjects of greatest interest. The information presented in this book should appeal to biochemists, cell biologists, and structural biologists.

Prediction of Protein Structures, Functions, and Interactions

Prediction of Protein Structures, Functions, and Interactions
  • Author : Janusz M. Bujnicki
  • Publisher :Unknown
  • Release Date :2008-12-23
  • Total pages :302
  • ISBN : 0470741902
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Summary : The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure prediction automated prediction of protein function from sequence template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling template-free prediction of three-dimensional protein structures quality assessment of protein models prediction of molecular interactions: from small ligands to large protein complexes macromolecular docking integrating prediction of structure, function, and interactions Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.

Nonlinear Systems, Vol. 2

Nonlinear Systems, Vol. 2
  • Author : Juan F. R. Archilla,Faustino Palmero,M. Carmen Lemos,Bernardo Sánchez-Rey,Jesús Casado-Pascual
  • Publisher :Unknown
  • Release Date :2017-12-21
  • Total pages :340
  • ISBN : 9783319722184
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Summary : This book presents an overview of the most recent advances in nonlinear science. It provides a unified view of nonlinear properties in many different systems and highlights many new developments. While volume 1 concentrates on mathematical theory and computational techniques and challenges, which are essential for the study of nonlinear science, this second volume deals with nonlinear excitations in several fields. These excitations can be localized and transport energy and matter in the form of breathers, solitons, kinks or quodons with very different characteristics, which are discussed in the book. They can also transport electric charge, in which case they are known as polarobreathers or solectrons. Nonlinear excitations can influence function and structure in biology, as for example, protein folding. In crystals and other condensed matter, they can modify transport properties, reaction kinetics and interact with defects. There are also engineering applications in electric lattices, Josephson junction arrays, waveguide arrays, photonic crystals and optical fibers. Nonlinear excitations are inherent to Bose-Einstein Condensates, constituting an excellent benchmark for testing their properties and providing a pathway for future discoveries in fundamental physics.

Manufacture Engineering, Quality and Production System II

Manufacture Engineering, Quality and Production System II
  • Author : Yiyi Zhouzhou
  • Publisher :Unknown
  • Release Date :2013-06-27
  • Total pages :860
  • ISBN : 9783038260783
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Summary : Selected, peer reviewed papers from the 2013 2nd International Conference on Manufacture Engineering, Quality and Production System (ICMEQP 2013), February 27-28, 2013, Hong Kong, China

Computational Science and Its Applications - ICCSA 2004

Computational Science and Its Applications - ICCSA 2004
  • Author : Antonio Laganà,Marina L. Gavrilova,Vipin Kumar,Youngsong Mun,C.J. Kenneth Tan,Osvaldo Gervasi
  • Publisher :Unknown
  • Release Date :2004-05-07
  • Total pages :1044
  • ISBN : 9783540220572
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Summary : The natural mission of Computational Science is to tackle all sorts of human problems and to work out intelligent automata aimed at alleviating the b- den of working out suitable tools for solving complex problems. For this reason ComputationalScience,thoughoriginatingfromtheneedtosolvethemostch- lenging problems in science and engineering (computational science is the key player in the ?ght to gain fundamental advances in astronomy, biology, che- stry, environmental science, physics and several other scienti?c and engineering disciplines) is increasingly turning its attention to all ?elds of human activity. In all activities, in fact, intensive computation, information handling, kn- ledge synthesis, the use of ad-hoc devices, etc. increasingly need to be exploited and coordinated regardless of the location of both the users and the (various and heterogeneous) computing platforms. As a result the key to understanding the explosive growth of this discipline lies in two adjectives that more and more appropriately refer to Computational Science and its applications: interoperable and ubiquitous. Numerous examples of ubiquitous and interoperable tools and applicationsaregiveninthepresentfourLNCSvolumescontainingthecontri- tions delivered at the 2004 International Conference on Computational Science and its Applications (ICCSA 2004) held in Assisi, Italy, May 14–17, 2004.

BIOINFORMATICS

BIOINFORMATICS
  • Author : VITTAL R. SRINIVAS
  • Publisher :Unknown
  • Release Date :2005-01-01
  • Total pages :280
  • ISBN : 8120328582
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Summary : Being an interdisciplinary subject, Bioinformatics is today covering a range of interest both among the students and teaching communities. Taking this increasing interest into account, this book gives a comprehensive introduction to the subject. The text not only deals with the basic concepts but it also emphasizes the technical and practical aspects of the subject. The book covers the computational tools in bioinformatics, algorithmic aspects as well as technological aspects. Besides it gives a clear exposition of Viterbi algorithm, Hidden Markov models, UPGMA, FM algorithm, heuristic, developing and using substitution matrices, HMMs and derivation of a number of standard formulae in information theory and statistics. Finally the text focusses on the technological aspects of bioinformatics such as sequencing through shot gun methods, microarrays, with a variety of unsupervised methods in data analysis with examples, as well as interdisciplinary research in systems biology. The book is primarily intended as a text for the students of Computer Science, Information Technology, undergraduate students of Bioinformatics, PGDCA and biological sciences and biotechnology. The book should also be of considerable interest for research scientist in Chemistry and Pharmacy.

Bioinformatics: Sequences, Structures, Phylogeny

Bioinformatics: Sequences, Structures, Phylogeny
  • Author : Asheesh Shanker
  • Publisher :Unknown
  • Release Date :2018-10-13
  • Total pages :402
  • ISBN : 9789811315626
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Summary : This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.

Proteolytic Enzymes

Proteolytic Enzymes
  • Author : Erwin E. Sterchi,Walter Stöcker
  • Publisher :Unknown
  • Release Date :2013-11-11
  • Total pages :366
  • ISBN : 9783642598166
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Summary : Following an overview on proteolytic enzyme assays, this text covers procedures on how to investigate and study proteases. It describes the use of specific restriction proteases as well as inhibitors of proteases to prevent unwanted proteolysis.

Protein Simulations

Protein Simulations
  • Author : Valerie Daggett
  • Publisher :Unknown
  • Release Date :2003-11-26
  • Total pages :459
  • ISBN : 9780080493787
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Summary : Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields * Ligand Binding * Protein Membrane Simulation * Enzyme Dynamics * Protein Folding and unfolding simulations