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Protein Folding in Silico

Protein Folding in Silico
Protein Folding Versus Protein Structure Prediction

by Irena Roterman-Konieczna

  • Publisher : Elsevier
  • Release : 2012-10-04
  • Pages : 240
  • ISBN : 1908818255
  • Language : En, Es, Fr & De
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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

Protein Folding in Silico

Protein Folding in Silico
Protein Folding Versus Protein Structure Prediction

by Irena Roterman-Konieczna

  • Publisher : Woodhead Publishing
  • Release : 2012-10-18
  • Pages : 240
  • ISBN : 9781907568176
  • Language : En, Es, Fr & De
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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

Protein Folding in Silico

Protein Folding in Silico
Protein Folding Versus Protein Structure Prediction

by Irena Roterman-Konieczna

  • Publisher : Woodhead Publishing
  • Release : 2017-11-13
  • Pages : 240
  • ISBN : 9780081016718
  • Language : En, Es, Fr & De
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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 predictionIntroduces a unique model based on experimental observationsDescribes various methods for the quantitative assessment of the presented models from the viewpoint of information theory

In Silico Study of Amyloid [beta]-protein Folding Relevant to Alzheimer's Disease

In Silico Study of Amyloid [beta]-protein Folding Relevant to Alzheimer's Disease
A Book

by Alfonso Ramon Lam Ng

  • Publisher : Unknown Publisher
  • Release : 2008
  • Pages : 204
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Systems Biology

Systems Biology
Functional Strategies of Living Organisms

by Leszek Konieczny,Irena Roterman-Konieczna,Paweł Spólnik

  • Publisher : Springer Science & Business Media
  • Release : 2013-10-01
  • Pages : 204
  • ISBN : 331901336X
  • Language : En, Es, Fr & De
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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
With Charts

by Frederick Douglas Hamblin

  • Publisher : Pergamon
  • Release : 1968
  • Pages : 73
  • ISBN : 0081029810
  • Language : En, Es, Fr & De
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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
A Book

by Irena Roterman-Konieczna

  • Publisher : Springer Science & Business Media
  • Release : 2012-10-19
  • Pages : 170
  • ISBN : 9400752849
  • Language : En, Es, Fr & De
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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
A Book

by Anonim

  • Publisher : Academic Press
  • Release : 2014-03-11
  • Pages : 488
  • ISBN : 0128003731
  • Language : En, Es, Fr & De
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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

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
A Book

by Eric J. Sorin

  • Publisher : Unknown Publisher
  • Release : 2007
  • Pages : 348
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Protein Folding

Protein Folding
An Introduction

by Claudio Gomes,Patricia Faisca

  • Publisher : Springer
  • Release : 2018-05-25
  • Pages : 100
  • ISBN : 331900882X
  • Language : En, Es, Fr & De
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This snapshot volume is designed to provide a smooth entry into the field of protein folding. Presented in a concise manner, each section introduces key concepts while providing a brief overview of the relevant literature. Outlook subsections will pinpoint specific aspects related to emerging methodologies, concepts and trends.

Combining in Vivo and in Silico Screening for Protein Stability

Combining in Vivo and in Silico Screening for Protein Stability
A Book

by Nora Hisham Barakat

  • Publisher : Unknown Publisher
  • Release : 2007
  • Pages : 167
  • ISBN : 9781109961799
  • Language : En, Es, Fr & De
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In the in vivo 'chimeric' screen a target protein is expressed as a fusion protein with a DNA binding domain fused at the N-terminus and a transactivation domain at the C-terminus. This three-component fusion protein acts as a functional transcription factor for a reporter gene. If the central target protein is relatively unstable it is more flexible and thereby allows the DNA binding domain and the transactivation domain to achieve an optimal orientation for transcriptional activation. Conversely, if the central target protein is highly stable it is too rigid to allow the DNA binding domain and the transactivation domain to achieve the proper orientation for transcriptional activation and thus is a less efficient transcription factor.

Multiscale Approaches to Protein Modeling

Multiscale Approaches to Protein Modeling
A Book

by Andrzej Kolinski

  • Publisher : Springer Science & Business Media
  • Release : 2010-10-13
  • Pages : 355
  • ISBN : 9781441968890
  • Language : En, Es, Fr & De
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The book gives a comprehensive review of the most advanced multiscale methods for protein structure prediction, computational studies of protein dynamics, folding mechanisms and macromolecular interactions. It approaches span a wide range of the levels of coarse-grained representations, various sampling techniques and variety of applications to biomedical and biophysical problems. This book is intended to be used as a reference book for those who are just beginning their adventure with biomacromolecular modeling but also as a valuable source of detailed information for those who are already experts in the field of biomacromolecular modeling and in related areas of computational biology or biophysics.

Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly

Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly
A Book

by Anonim

  • Publisher : Academic Press
  • Release : 2020-03-05
  • Pages : 552
  • ISBN : 0128211377
  • Language : En, Es, Fr & De
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Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly, Volume 170 in the Progress in Molecular Biology and Translational Science series, provides the most topical, informative and exciting monographs available on a wide variety of research topics. The series includes in-depth knowledge on the molecular biological aspects of organismal physiology, with this release including chapters on Pairwise-Additive and Polarizable Atomistic Force Fields for Molecular Dynamics Simulations of Proteins, Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers, Enhanced sampling and free energy methods, and much more. Includes comprehensive coverage on molecular biology Presents ample use of tables, diagrams, schemata and color figures to enhance the reader's ability to rapidly grasp the information provided Contains contributions from renowned experts in the field

In Silico Technologies in Drug Target Identification and Validation

In Silico Technologies in Drug Target Identification and Validation
A Book

by Darryl Leon,Scott Markel

  • Publisher : CRC Press
  • Release : 2006-06-13
  • Pages : 504
  • ISBN : 1420015737
  • Language : En, Es, Fr & De
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The pharmaceutical industry relies on numerous well-designed experiments involving high-throughput techniques and in silico approaches to analyze potential drug targets. These in silico methods are often predictive, yielding faster and less expensive analyses than traditional in vivo or in vitro procedures. In Silico Technologies in Drug Target Identification and Validation addresses the challenge of testing a growing number of new potential targets and reviews currently available in silico approaches for identifying and validating these targets. The book emphasizes computational tools, public and commercial databases, mathematical methods, and software for interpreting complex experimental data. The book describes how these tools are used to visualize a target structure, identify binding sites, and predict behavior. World-renowned researchers cover many topics not typically found in most informatics books, including functional annotation, siRNA design, pathways, text mining, ontologies, systems biology, database management, data pipelining, and pharmacogenomics. Covering issues that range from prescreening target selection to genetic modeling and valuable data integration, In Silico Technologies in Drug Target Identification and Validation is a self-contained and practical guide to the various computational tools that can accelerate the identification and validation stages of drug target discovery and determine the biological functionality of potential targets more effectively. Daniel E. Levy, editor of the Drug Discovery Series, is the founder of DEL BioPharma, a consulting service for drug discovery programs. He also maintains a blog that explores organic chemistry.

Machine Learning Paradigms

Machine Learning Paradigms
Advances in Data Analytics

by George A. Tsihrintzis,Dionisios N. Sotiropoulos,Lakhmi C. Jain

  • Publisher : Springer
  • Release : 2018-07-03
  • Pages : 370
  • ISBN : 3319940309
  • Language : En, Es, Fr & De
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This book explores some of the emerging scientific and technological areas in which the need for data analytics arises and is likely to play a significant role in the years to come. At the dawn of the 4th Industrial Revolution, data analytics is emerging as a force that drives towards dramatic changes in our daily lives, the workplace and human relationships. Synergies between physical, digital, biological and energy sciences and technologies, brought together by non-traditional data collection and analysis, drive the digital economy at all levels and offer new, previously-unavailable opportunities. The need for data analytics arises in most modern scientific disciplines, including engineering; natural-, computer- and information sciences; economics; business; commerce; environment; healthcare; and life sciences. Coming as the third volume under the general title MACHINE LEARNING PARADIGMS, the book includes an editorial note (Chapter 1) and an additional 12 chapters, and is divided into five parts: (1) Data Analytics in the Medical, Biological and Signal Sciences, (2) Data Analytics in Social Studies and Social Interactions, (3) Data Analytics in Traffic, Computer and Power Networks, (4) Data Analytics for Digital Forensics, and (5) Theoretical Advances and Tools for Data Analytics. This research book is intended for both experts/researchers in the field of data analytics, and readers working in the fields of artificial and computational intelligence as well as computer science in general who wish to learn more about the field of data analytics and its applications. An extensive list of bibliographic references at the end of each chapter guides readers to probe further into the application areas of interest to them.

Combining in Vivo and in Silico Screening for Protein Stability

Combining in Vivo and in Silico Screening for Protein Stability
A Book

by Anonim

  • Publisher : Unknown Publisher
  • Release : 2007
  • Pages : 304
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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In any protein design endeavor, thermal stability is an important issue. Increasing protein stability is currently one of the main goals of the field of protein design as well as the biomedical industry. It is important for developing stable protein-based therapeutics and ultimately enhances our understanding of the principles of protein folding. The overall goal of my project is to develop and combine in vivo and in silico screening and analysis to select stable proteins from a large combinatorial library of proteins. Our in vivo screening method is based solely on the stability of the test proteins, and is independent of protein function. In addition, the mutant variants obtained from the in vivo screen were further analyzed and screened in silico with the ORBIT protein design package. In the in vivo 'chimeric' screen a target protein is expressed as a fusion protein with a DNA binding domain fused at the N-terminus and a transactivation domain at the C-terminus. This three-component fusion protein acts as a functional transcription factor for a reporter gene. If the central target protein is relatively unstable it is more flexible and thereby allows the DNA binding domain and the transactivation domain to achieve an optimal orientation for transcriptional activation. Conversely, if the central target protein is highly stable it is too rigid to allow the DNA binding domain and the transactivation domain to achieve the proper orientation for transcriptional activation and thus is a less efficient transcription factor. To supplement the results obtained from the in vivo screen we also use the ORBIT suite of protein design algorithms to computationally generate stability variants. These algorithms enable one to mutate specific residues while keeping the remainder wild-type. Discrete sets of side chain rotamers are considered in the calculation and an empirical potential energy function is used to calculate the energies between rotamer pairs. The energies are subjected to a very fast side chain selection algorithm, based on the Dead-End Elimination theorem, which ultimately returns the global minimum energy conformation. We successfully demonstrated the ability of the in vivo chimeric stability screen and in silico ORBIT screen to generate novel protein variants with improved thermal stability.

Parallel Computing

Parallel Computing
Architectures, Algorithms, and Applications

by Christian Bischof

  • Publisher : IOS Press
  • Release : 2008
  • Pages : 804
  • ISBN : 158603796X
  • Language : En, Es, Fr & De
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Untitled

Untitled
A Book

by Anonim

  • Publisher : IOS Press
  • Release : 2021
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Structure and Action of Molecular Chaperones

Structure and Action of Molecular Chaperones
Machines that Assist Protein Folding in the Cell

by Lila M Gierasch,Arthur L Horwich,Christine Slingsby,Sue Wickner,David Agard

  • Publisher : World Scientific
  • Release : 2016-08-08
  • Pages : 129
  • ISBN : 9814749346
  • Language : En, Es, Fr & De
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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.

Total Chemical Synthesis of Proteins

Total Chemical Synthesis of Proteins
A Book

by Ashraf Brik,Philip Dawson,Lei Liu

  • Publisher : John Wiley & Sons
  • Release : 2021-02-23
  • Pages : 624
  • ISBN : 3527823573
  • Language : En, Es, Fr & De
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How to synthesize native and modified proteins in the test tube With contributions from a panel of experts representing a range of disciplines, Total Chemical Synthesis of Proteins presents a carefully curated collection of synthetic approaches and strategies for the total synthesis of native and modified proteins. Comprehensive in scope, this important reference explores the three main chemoselective ligation methods for assembling unprotected peptide segments, including native chemical ligation (NCL). It includes information on synthetic strategies for the complex polypeptides that constitute glycoproteins, sulfoproteins, and membrane proteins, as well as their characterization. In addition, important areas of application for total protein synthesis are detailed, such as protein crystallography, protein engineering, and biomedical research. The authors also discuss the synthetic challenges that remain to be addressed. This unmatched resource: Contains valuable insights from the pioneers in the field of chemical protein synthesis Presents proven synthetic approaches for a range of protein families Explores key applications of precisely controlled protein synthesis, including novel diagnostics and therapeutics Written for organic chemists, biochemists, biotechnologists, and molecular biologists, Total Chemical Synthesis of Proteins provides key knowledge for everyone venturing into the burgeoning field of protein design and synthetic biology.