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Methods For Structural Analysis Of Protein Pharmaceuticals

Author : Wim Jiskoot
ISBN : 0971176728
Genre : Medical
File Size : 74. 33 MB
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Protein pharmaceuticals form a fast-growing category in the arsenal of drugs. This book explores the nature of different analytical techniques and the way in which they are related to pharmaceutical proteins. In addition to serving the analytical chemist, this book is needed by the formulation scientist who is responsible for design and formulation of a pharmaceutical protein that can be monitored during production and over time.

Protein Structure

Author : Daniel Chasman
ISBN : 9780824748166
Genre : Medical
File Size : 77. 5 MB
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This text offers in-depth perspectives on every aspect of protein structure identification, assessment, characterization, and utilization, for a clear understanding of the diversity of protein shapes, variations in protein function, and structure-based drug design. The authors cover numerous high-throughput technologies as well as computational methods to study protein structures and residues. A valuable reference, this book reflects current trends in the effort to solve new structures arising from genome initiatives, details methods to detect and identify errors in the prediction of protein structural models, and outlines challenges in the conversion of routine processes into high-throughput platforms.

Membrane Proteins Production For Structural Analysis

Author : Isabelle Mus-Veteau
ISBN : 9781493906628
Genre : Science
File Size : 22. 37 MB
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This book updates the latest development in production, stabilization and structural analysis techniques of membrane proteins. This field has made significant advances since the elucidation of the first 3-D structure of a recombinant G Protein Coupled Receptor (GPCR), rhodopsin, with the structure of several more GPCRs having been solved in the past five years. In fact, the 2012 Nobel Prize in Chemistry was awarded for groundbreaking discoveries on the inner workings of GPCRs. This book is essential reading for all researchers, biochemists and crystallographers working with membrane proteins, who are interested by the structural characterization of their favorite protein and who wish to follow the expression, migration, modifications and recycling of a membrane protein.

Mathematical Methods For Protein Structure Analysis And Design

Author : Concettina Guerra
ISBN : 9783540448273
Genre : Mathematics
File Size : 21. 3 MB
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The papers collected in this volume reproduce contributions by leading sch- arstoaninternationalschoolandworkshopwhichwasorganizedandheldwith thegoaloftakinga snapshotofadiscipline undertumultuous growth. Indeed, the area of protein folding, docking and alignment is developing in response to needs for a mix of heterogeneous expertise spanning biology, chemistry, mathematics, computer science, and statistics, among others. Some of the problems encountered in this area are not only important for the scienti?c challenges they pose, but also for the opportunities they disclose intermsofmedicalandindustrialexploitation. Atypicalexampleiso?eredby protein-drug interaction (docking), a problem posing daunting computational problems at the crossroads of geometry, physics and chemistry, and, at the same time, a problem with unimaginable implications for the pharmacopoeia of the future. The schoolfocused on problems posed by the study of the mechanisms - hind protein folding, and explored di?erent ways of attacking these problems under objective evaluations of the methods. Together with a relatively small core of consolidated knowledge and tools, important re?ections were brought to this e?ort by studies in a multitude of directions and approaches. It is obviously impossible to predict which, if any, among these techniques will prove completely successful, but it is precisely the implicit dialectic among them that best conveys the current ?avor of the ?eld. Such unique diversity and richness inspired the format of the meeting, and also explains the slight departure of the present volume from the typical format in this series: the exposition of the current sediment is complemented here by a selection of quali?ed specialized contributions.

From Protein Structure To Function With Bioinformatics

Author : Daniel J. Rigden
ISBN : 9789402410693
Genre : Science
File Size : 46. 23 MB
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This book is about protein structural bioinformatics and how it can help understand and predict protein function. It covers structure-based methods that can assign and explain protein function based on overall folds, characteristics of protein surfaces, occurrence of small 3D motifs, protein-protein interactions and on dynamic properties. Such methods help extract maximum value from new experimental structures, but can often be applied to protein models. The book also, therefore, provides comprehensive coverage of methods for predicting or inferring protein structure, covering all structural classes from globular proteins and their membrane-resident counterparts to amyloid structures and intrinsically disordered proteins. The book is split into two broad sections, the first covering methods to generate or infer protein structure, the second dealing with structure-based function annotation. Each chapter is written by world experts in the field. The first section covers methods ranging from traditional homology modelling and fold recognition to fragment-based ab initio methods, and includes a chapter, new for the second edition, on structure prediction using evolutionary covariance. Membrane proteins and intrinsically disordered proteins are each assigned chapters, while two new chapters deal with amyloid structures and means to predict modes of protein-protein interaction. The second section includes chapters covering functional diversity within protein folds and means to assign function based on surface properties and recurring motifs. Further chapters cover the key roles of protein dynamics in protein function and use of automated servers for function inference. The book concludes with two chapters covering case studies of structure prediction, based respectively on crystal structures and protein models, providing numerous examples of real-world usage of the methods mentioned previously. This book is targeted at postgraduate students and academic researchers. It is most obviously of interest to protein bioinformaticians and structural biologists, but should also serve as a guide to biologists more broadly by highlighting the insights that structural bioinformatics can provide into proteins of their interest.

Protein Protein Complexes

Author : Martin Zacharias
ISBN : 9781908978547
Genre : Science
File Size : 46. 26 MB
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Given the immense progress achieved in elucidating protein–protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein–protein interactions from the analysis of protein–protein complex structures and interfaces. What are the driving forces for protein–protein association? How can we extract the mechanism of specific recognition from studying protein–protein interfaces? How can this knowledge be used to predict and design protein–protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein–protein interactions, and how can we influence protein–protein interactions by mutagenesis and small-molecule drugs or peptide mimetics? The book consists of about 15 review chapters, written by experts, on the characterization of protein–protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein–protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein–protein complex structures (docking and homology modeling of complexes, etc.) and design of protein–protein interactions. It serves as a bridge between studying/analyzing protein–protein complex structures (interfaces), predicting interactions, and influencing/designing interactions. Contents: X-ray Study of Protein–Protein Complexes and Analysis of Interfaces (J Janin)A Structural Perspective on Protein–Protein Interactions in Macromolecular Assemblies (R P Bahadur)Energetics of Protein–Protein Interactions (I Jelezarov)Kinetics of Biomacromolecular Complex Formation: Theory and Experiment (G V Pachov et al.)Evolutionary Trace of Protein Functional Determinants (O Lichtarge)Protein–Protein Docking (A Saladin & C Prevost)Data-driven Docking: Using External Information to Spark the Biomolecular Rendez-vous (A S J Melquiond & A M J J Bonvin)High-Resolution Protein–Protein Docking (N London & O Schueler-Furman)Scoring and Refinement of Predicted Protein–Protein Complexes (M Zacharias)Motif-medicated Protein Interactions and Their Role in Disease (H Dinkel & H Sticht)Prediction and Calculation of Protein–Protein Binding Affinities and Mutation Effects (S Fiorucci et al.)Small-molecule Inhibitors of Protein–Protein Interactions (T Berg)Protein Dynamics and Drug Design: The Role of Molecular Simulations (G Morra et al.) Readership: Graduate students and researchers in bioinformatics and computational biology, biophysics, biochemistry, structural biology, and drug design. Keywords:Protein–Protein Interactions;Protein–Protein Complexes;Protein Design;Binding Interface, Protein Evolution;Structural Bioinformatics;Protein Interaction NetworkKey Features:Covers protein–protein interactions at the structural level in great detailDescribes the structure of protein–protein complexes, and also gives insight into the mechanism of complex formation and the forces that drive complex formationCovers to some degree the emerging field of designing new protein–protein interactions, i.e. how to interfere with protein–protein interactions that are of medical importance through drug design

Computational Methods For Protein Structure Prediction And Modeling

Author : Ying Xu
ISBN : 9780387683720
Genre : Science
File Size : 52. 92 MB
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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.

Introduction To Computational Proteomics

Author : Golan Yona
ISBN : 9781420010770
Genre : Mathematics
File Size : 89. 36 MB
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Introduction to Computational Proteomics introduces the field of computational biology through a focused approach that tackles the different steps and problems involved with protein analysis, classification, and meta-organization. The book starts with the analysis of individual entities and works its way through the analysis of more complex entitie

Protein Structure By Distance Analysis

Author : Henrik Bohr
ISBN : 4274022633
Genre : Distance geometry
File Size : 44. 19 MB
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Protein Structure Prediction

Author : Igor F. Tsigelny
ISBN : 096368177X
Genre : Science
File Size : 75. 17 MB
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Protein Engineering And Design

Author : Sheldon J. Park
ISBN : 1420076590
Genre : Medical
File Size : 58. 75 MB
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Experimental protein engineering and computational protein design are broad but complementary strategies for developing proteins with altered or novel structural properties and biological functions. By describing cutting-edge advances in both of these fields, Protein Engineering and Design aims to cultivate a synergistic approach to protein science

Bioinformatics A Primer

Author : P. Narayanan
ISBN : 9788122416107
Genre : Bioinformatics
File Size : 88. 30 MB
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Bioinformatics Is The Bridge Between Experimental Data In Diverse Biologically Related Disciplines And Extrapolation Of Information, By Computational Analysis, About How The Systems And Processes Function. The Central Aims Are : (I) Elucidation (By Experimental Methods) Of Structural Features Of The Biological Entities (Proteins, Nucleic Acids Etc.), (Ii) Application Of Computational Tools And Approaches To Study Of Information Content, Organization, And Processing In Biological Systems, (Iii) Application Of Medical And Health Data At The Molecular Level (Biomedinformatics), Annotation Of Structural And Chemical Characteristics In Molecular And Drug Design (Cheminformatics). Thus, It Requires Trans-Disciplinary Collaboration Between Biophysicists, Drug Chemists, Molecular Biologists, Biomedical And Computer-Aided Modeling Experts.Acquisition Of High-Throughput Biological Data (E.G. From The Genomic Projects) At Fast Rate Has Ushered In Computer-Intensive Data Analysis (In Silico Analysis). But, Considerable Algorithmic Complexity Of Biological Systems Requires A Vast Of Amount Of Detailed Information (Experimental And Computational) At The Cellular And Molecular Levels For Their Complete Description. Therefore, There Is A Need For Books In This Subject With Due Emphasis On Both Experimental As Well As Computational Aspects.With These Broad Objectives In Mind, The Material Contents Of This Book Are Organized Under-Molecular Biophysics, Experimental Methods Of Structure Elucidation, Database Search, Data Mining And Analysis, Computational Methods Of Structure Prediction, And Rational Molecular/Drug Design (Molecular Engineering) And Validation-, With Easy Interface Between These Areas And Various Chapters. Ample Tables And Figures Are Intended To Facilitate The Readers An Insight To The Structure-Function Features At The Molecular Level. Exercise Modules And Bibliography For Each Chapter, And Glossary Are Aimed At Providing The Reader Wider Perception And Insight To The Subject Matter, And Scientific And Technical Terms. Index Is Provided To Help An Easy Access To The Words And Topics To The Subject Matter.

Methods In Proteome And Protein Analysis

Author : Roza Maria Kamp
ISBN : 3540202226
Genre : Science
File Size : 48. 63 MB
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Following the succesful publication of "Proteome and Protein Analysis" in 2000, which was based on a former MPSA (Methods in Protein Structure Analysis) conference, "Methods in Proteome and Protein Analysis" presents the most interesting papers from the 14th MPSA meeting. Selected contributions discuss the latest techniques and approaches for analysing protein and proteome structures. Major topics include: protein and peptide sample preparation and separation new reagent for protein sequence analysis mass spectrometry in protein research analysis of posttranslational modification protein-protein interaction using MALDI-MS manipulation of genome or functional compositon trap structure-function correlation study using optical biosensors of microcolorimetrical techniques structural proteomics as NMR or fluorescence polarization study the classification and prediction of structure or functional sites in silico analysis of proteins and proteomes increasing throughput and data quality for proteomics

Molecular Design And Modeling

Author : John Joseph Langone
ISBN : 012182103X
Genre : Medical
File Size : 54. 64 MB
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Computer-based design and modeling, computational approaches, and instrumental methods for elucidating molecular mechanisms of protein folding and ligand-acceptor interactions are included in Volumes 202 and 203, as are genetic and chemical methods for the production of functional molecules including antibodies and antigens, enzymes, receptors, nucleic acids and polysaccharides, and drugs.

Multiscale Approaches To Protein Modeling

Author : Andrzej Kolinski
ISBN : 144196889X
Genre : Science
File Size : 40. 65 MB
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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.

Methods In Protein Structure And Stability Analysis Conformational Stability Size Shape And Surface Of Protein Molecules

Author : Vladimir N. Uversky
ISBN : 1600217044
Genre : Science
File Size : 43. 28 MB
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Protein research is a frontier field in science. Proteins are widely distributed in plants and animals and are the principal constituents of the protoplasm of all cells, and consist essentially of combinations of a-amino acids in peptide linkages. Twenty different amino acids are commonly found in proteins, and serve as enzymes, structural elements, hormones, immunoglobulins, etc., and are involved throughout the body, and in photosynthesis. This book gathers new leading-edge research from throughout the world in this exciting and exploding field of research.

Structural Bioinformatics

Author : Jenny Gu
ISBN : 9780470181058
Genre : Computers
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The second edition of this successful text expands on the depth and scope of the topic by bringing together many of the world's experts to provide a view of the current state of the field suitable for advanced undergraduate students, graduate students and beyond. The book begins with a description of the principles of protein, DNA and RNA structure, the methods used to collect the data, and how the data are represented, visualized and stored. With these prerequisites the comparative analysis of structure reveals classification schemes and how they are used in studies ranging from evolution to structure prediction. The physical properties of structure are explored to understand, for example, how macromolecules move and interact with each other and with ligands, offering insights into how drug discovery is undertaken and how structure can provide the details needed to understand complex molecular interactions important in fields such as immunology and systems biology. Finally, structural genomics reveals insight into the future role of structural bioinformatics where features, including function, are systematically assigned and the structural basis of complete organisms begin to emerge.

Markov State Models For Protein And Rna Folding

Author :
ISBN : STANFORD:ky974bm1455
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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.

Computer Assisted Modeling

Author : National Research Council
ISBN : 9780309062282
Genre : Computers
File Size : 90. 59 MB
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In much of biology, the search for understanding the relation between structure and function is now taking place at the macromolecular level. Proteins, nucleic acids, and polysaccharides are macromolecule--polymers formed from families of simpler subunits. Because of their size and complexity, the polymers are capable of both inter- and intramolecular interactions. These interactions confer upon the polymers distinctive three-dimensional shapes. These tertiary configurations, in turn, determine the function of the macromolecule. Computers have become so inextricably involved in empirical studies of three-dimensional macromolecular structure that mathematical modeling, or theory, and experimental approaches are interrelated aspects of a single enterprise.

Infrared And Raman Spectroscopy Of Biological Materials

Author : Hans-Ulrich Gremlich
ISBN : 0824704096
Genre : Science
File Size : 76. 97 MB
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Infrared and Raman Spectroscopy of Biological Materials facilitates a comprehensive and through understanding of the latest developments in vibrational spectroscopy. It contains explains key breakthroughs in the methodologies and techniques for infrared, near-infrared, and Raman spectroscopy. Topics include qualitative and quantitative analysis, biomedical applications, vibrational studies of enzymatic catalysis, and chemometrics.

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