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Exploring Protein Secondary Structure
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Book Synopsis Exploring Protein Structure: Principles and Practice by : Tim Skern
Download or read book Exploring Protein Structure: Principles and Practice written by Tim Skern and published by Springer. This book was released on 2018-07-04 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook introduces the basics of protein structure and logically explains how to use online software to explore the information in protein structure databases. Readers will find easily understandable, step-by step exercises and video-trainings to support them in grasping the fundamental concepts. After reading this book, readers will have the skills required to independently explore and analyze macromolecular structures, will be versed in extracting information from protein databases and will be able to visualize protein structures using specialized software and on-line algorithms. This book is written for advanced undergraduates and PhD students wishing to use information from structural biology in their assignments and research and will be a valuable source of information for all those interested in applied and theoretical aspects of structural biology.
Book Synopsis Exploring Protein Secondary Structure by : Ken Tse-yau Lau
Download or read book Exploring Protein Secondary Structure written by Ken Tse-yau Lau and published by . This book was released on 1997 with total page 178 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Prediction of Protein Secondary Structure by : Yaoqi Zhou
Download or read book Prediction of Protein Secondary Structure written by Yaoqi Zhou and published by Humana. This book was released on 2018-06-08 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough volume explores predicting one-dimensional functional properties, functional sites in particular, from protein sequences, an area which is getting more and more attention. Beginning with secondary structure prediction based on sequence only, the book continues by exploring secondary structure prediction based on evolution information, prediction of solvent accessible surface areas and backbone torsion angles, model building, global structural properties, functional properties, as well as visualizing interior and protruding regions in proteins. Written for the highly successful Methods in Molecular Biology series, the chapters include the kind of detail and implementation advice to ensure success in the laboratory. Practical and authoritative, Prediction of Protein Secondary Structure serves as a vital guide to numerous state-of-the-art techniques that are useful for computational and experimental biologists.
Book Synopsis Computer Assisted Modeling by : National Research Council
Download or read book Computer Assisted Modeling written by National Research Council and published by National Academies Press. This book was released on 1987-02-01 with total page 186 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Biology of The Cell by : Bruce Alberts
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Bioinformatics by : M. Michael Gromiha
Download or read book Protein Bioinformatics written by M. Michael Gromiha and published by Academic Press. This book was released on 2011-04-21 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the most pressing tasks in biotechnology today is to unlock the function of each of the thousands of new genes identified every day. Scientists do this by analyzing and interpreting proteins, which are considered the task force of a gene. This single source reference covers all aspects of proteins, explaining fundamentals, synthesizing the latest literature, and demonstrating the most important bioinformatics tools available today for protein analysis, interpretation and prediction. Students and researchers of biotechnology, bioinformatics, proteomics, protein engineering, biophysics, computational biology, molecular modeling, and drug design will find this a ready reference for staying current and productive in this fast evolving interdisciplinary field. Explains all aspects of proteins including sequence and structure analysis, prediction of protein structures, protein folding, protein stability, and protein interactions Presents a cohesive and accessible overview of the field, using illustrations to explain key concepts and detailed exercises for students.
Book Synopsis Introduction to Proteins by : Amit Kessel
Download or read book Introduction to Proteins written by Amit Kessel and published by CRC Press. This book was released on 2018-03-22 with total page 1423 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins for students, faculty, and researchers at all levels. The book covers proteins and enzymes across a wide range of contexts and applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. Each chapter includes a Summary, Exercies, and References. New features in the thoroughly-updated second edition include: A brand-new chapter on enzymatic catalysis, describing enzyme biochemistry, classification, kinetics, thermodynamics, mechanisms, and applications in medicine and other industries. These are accompanied by multiple animations of biochemical reactions and mechanisms, accessible via embedded QR codes (which can be viewed by smartphones) An in-depth discussion of G-protein-coupled receptors (GPCRs) A wider-scale description of biochemical and biophysical methods for studying proteins, including fully accessible internet-based resources, such as databases and algorithms Animations of protein dynamics and conformational changes, accessible via embedded QR codes Additional features Extensive discussion of the energetics of protein folding, stability and interactions A comprehensive view of membrane proteins, with emphasis on structure-function relationship Coverage of intrinsically unstructured proteins, providing a complete, realistic view of the proteome and its underlying functions Exploration of industrial applications of protein engineering and rational drug design Each chapter includes a Summary, Exercies, and References Approximately 300 color images Downloadable solutions manual available at www.crcpress.com For more information, including all presentations, tables, animations, and exercises, as well as a complete teaching course on proteins' structure and function, please visit the author's website: http://ibis.tau.ac.il/wiki/nir_bental/index.php/Introduction_to_Proteins_Book. Praise for the first edition "This book captures, in a very accessible way, a growing body of literature on the structure, function and motion of proteins. This is a superb publication that would be very useful to undergraduates, graduate students, postdoctoral researchers, and instructors involved in structural biology or biophysics courses or in research on protein structure-function relationships." --David Sheehan, ChemBioChem, 2011 "Introduction to Proteins is an excellent, state-of-the-art choice for students, faculty, or researchers needing a monograph on protein structure. This is an immensely informative, thoroughly researched, up-to-date text, with broad coverage and remarkable depth. Introduction to Proteins would provide an excellent basis for an upper-level or graduate course on protein structure, and a valuable addition to the libraries of professionals interested in this centrally important field." --Eric Martz, Biochemistry and Molecular Biology Education, 2012
Book Synopsis Protein Supersecondary Structures by : Alexander E. Kister
Download or read book Protein Supersecondary Structures written by Alexander E. Kister and published by Humana Press. This book was released on 2019-04-04 with total page 438 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition volume expands on the previous edition with an update on the latest developments in the field and new techniques used to study secondary and supersecondary structures (SSS) in proteins. Chapters in this book discuss topics such as sequence and structural features of different SSS elements; software used for the automatic annotation of secondary structure elements in proteins; the new developments in secondary and SSS prediction and the modern approaches for energy landscape calculation; protein misfolding and amyloid structural formation; analysis of ‘transformer proteins’; discovery of the structure of the hydrophobic nucleus; and discussions of the main principles of protein structures formation. The contributing authors of the volume are the eminent experts in the field of protein research and bioinformatics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and authoritative, Protein Supersecondary Structures: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about the relationship between amino acids sequences and protein structures, the evolution of proteins and the dynamics of protein formation.
Book Synopsis Exploring the Impact of Pretrained Bidirectional Language Models on Protein Secondary Structure Prediction by : Dillon G. Daudert
Download or read book Exploring the Impact of Pretrained Bidirectional Language Models on Protein Secondary Structure Prediction written by Dillon G. Daudert and published by . This book was released on 2018 with total page 56 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein secondary structure prediction (PSSP) involves determining the local conformations of the peptide backbone in a folded protein, and is often the first step in resolving a protein's global folded structure. Accurate structure prediction has important implications for understanding protein function and de novo protein design, with progress in recent years being driven by the application of deep learning methods such as convolutional and recurrent neural networks. Language models pretrained on large text corpora have been shown to learn useful representations for feature extraction and transfer learning across problem domains in natural language processing, most notably in instances where the amount of labeled data for supervised learning is limited. This presents the possibility that pretrained language models can have a positive impact on PSSP, as sequenced proteins vastly outnumber those proteins whose folded structures are known. In this work, we pretrain a large bidirectional language model (BDLM) on a nonredundant dataset of one million protein sequences gathered from UniRef50. The outputs and intermediate layer activations of this BDLM are incorporated into a bidirectional recurrent neural network (RNN) trained to predict secondary structure. We provide an empirical assessment of the impact the representations learned by our pretrained model have on PSSP and analyze the mutual information of these representations with secondary structure labels.
Book Synopsis Prediction of Protein Structure and the Principles of Protein Conformation by : G.D. Fasman
Download or read book Prediction of Protein Structure and the Principles of Protein Conformation written by G.D. Fasman and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 796 pages. Available in PDF, EPUB and Kindle. Book excerpt: The prediction of the conformation of proteins has developed from an intellectual exercise into a serious practical endeavor that has great promise to yield new stable enzymes, products of pharmacological significance, and catalysts of great potential. With the application of predic tion gaining momentum in various fields, such as enzymology and immunology, it was deemed time that a volume be published to make available a thorough evaluation of present methods, for researchers in this field to expound fully the virtues of various algorithms, to open the field to a wider audience, and to offer the scientific public an opportunity to examine carefully its successes and failures. In this manner the practitioners of the art could better evaluate the tools and the output so that their expectations and applications could be more realistic. The editor has assembled chapters by many of the main contributors to this area and simultaneously placed their programs at three national resources so that they are readily available to those who wish to apply them to their personal interests. These algorithms, written by their originators, when utilized on pes or larger computers, can instantaneously take a primary amino acid sequence and produce a two-or three-dimensional artistic image that gives satisfaction to one's esthetic sensibilities and food for thought concerning the structure and function of proteins. It is in this spirit that this volume was envisaged.
Book Synopsis Protein Families by : Christine A. Orengo
Download or read book Protein Families written by Christine A. Orengo and published by John Wiley & Sons. This book was released on 2014-02-03 with total page 566 pages. Available in PDF, EPUB and Kindle. Book excerpt: New insights into the evolution and nature of proteins Exploring several distinct approaches, this book describes the methods for comparing protein sequences and protein structures in order to identify homologous relationships and classify proteins and protein domains into evolutionary families. Readers will discover the common features as well as the key philosophical differences underlying the major protein classification systems, including Pfam, Panther, SCOP, and CATH. Moreover, they'll discover how these systems can be used to understand the evolution of protein families as well as understand and predict the degree to which structural and functional information are shared between relatives in a protein family. Edited and authored by leading international experts, Protein Families offers new insights into protein families that are important to medical research as well as protein families that help us understand biological systems and key biological processes such as cell signaling and the immune response. The book is divided into three sections: Section I: Concepts Underlying Protein Family Classification reviews the major strategies for identifying homologous proteins and classifying them into families. Section II: In-Depth Reviews of Protein Families focuses on some fascinating super protein families for which we have substantial amounts of sequence, structural and functional data, making it possible to trace the emergence of functionally diverse relatives. Section III: Review of Protein Families in Important Biological Systems examines protein families associated with a particular biological theme, such as the cytoskeleton. All chapters are extensively illustrated, including depictions of evolutionary relationships. References at the end of each chapter guide readers to original research papers and reviews in the field. Covering protein family classification systems alongside detailed descriptions of select protein families, this book offers biochemists, molecular biologists, protein scientists, structural biologists, and bioinformaticians new insight into the evolution and nature of proteins.
Book Synopsis Protein Structure by Distance Analysis by : Henrik Bohr
Download or read book Protein Structure by Distance Analysis written by Henrik Bohr and published by IOS Press. This book was released on 1994 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction [electronic Resource] by : Tang, Thomas Cheuk Kai
Download or read book Discovering Protein Sequence-Structure Motifs and Two Applications to Structural Prediction [electronic Resource] written by Tang, Thomas Cheuk Kai and published by University of Waterloo. This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis investigates the correlations between short protein peptide sequences and local tertiary structures. In particular, it introduces a novel algorithm for partitioning short protein segments into clusters of local sequence-structure motifs, and demonstrates that these motif clusters contain useful structural information via two applications to structural prediction. The first application utilizes motif clusters to predict local protein tertiary structures. A novel dynamic programming algorithm that performs comparably with some of the best existing algorithms is described. The second application exploits the capability of motif clusters in recognizing regular secondary structures to improve the performance of secondary structure prediction based on Support Vector Machines. Empirical results show significant improvement in overall prediction accuracy with no performance degradation in any specific aspect being measured. The encouraging results obtained illustrate the great potential of using local sequence-structure motifs to tackle protein structure predictions and possibly other important problems in computational biology.
Book Synopsis A Segment Based Approach to Protein Secondary Structure Prediction by : Bruce Ira Cohen
Download or read book A Segment Based Approach to Protein Secondary Structure Prediction written by Bruce Ira Cohen and published by . This book was released on 1991 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Mathematical Methods for Protein Structure Analysis and Design by : Concettina Guerra
Download or read book Mathematical Methods for Protein Structure Analysis and Design written by Concettina Guerra and published by Springer Science & Business Media. This book was released on 2003-06-25 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Protein Structure and Function by : Gregory A. Petsko
Download or read book Protein Structure and Function written by Gregory A. Petsko and published by New Science Press. This book was released on 2004 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Each title in the 'Primers in Biology' series is constructed on a modular principle that is intended to make them easy to teach from, to learn from, and to use for reference.
Book Synopsis Biological Sequence Analysis by : Richard Durbin
Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.
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