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Author : Christopher Lung Kong Tang
Publisher :
ISBN 13 :
Total Pages : 254 pages
Book Rating : 4.:/5 (259 download)
Download or read book Computational Studies of Proteins and Nucleic Acids written by Christopher Lung Kong Tang and published by . This book was released on 2008 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Studies of Proteins and Nucleic Acids: On Pk(a) Calculations in RNA and the Use of Structure to Improve Sequence Alignments written by and published by . This book was released on 2008 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational studies of proteins and nucleic acids: On pk(a) calculations in RNA and the use of structure to improve sequence alignments.
Author : Tiba Aynechi
Publisher :
ISBN 13 :
Total Pages : 410 pages
Book Rating : 4.:/5 (85 download)
Download or read book Computational Studies Characterizing the Information Encoded in Protein Structures and Sequences written by Tiba Aynechi and published by . This book was released on 2005 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Jirí Šponer
Publisher : Springer
ISBN 13 : 9789048171958
Total Pages : 0 pages
Book Rating : 4.1/5 (719 download)
Download or read book Computational studies of RNA and DNA written by Jirí Šponer and published by Springer. This book was released on 2010-11-25 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book integrates modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed.
Author : Ying Xu
Publisher : Springer Science & Business Media
ISBN 13 : 0387688250
Total Pages : 335 pages
Book Rating : 4.3/5 (876 download)
Download or read book Computational Methods for Protein Structure Prediction and Modeling written by Ying Xu and published by Springer Science & Business Media. This book was released on 2010-05-05 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume Two of this two-volume sequence presents a comprehensive overview of protein structure prediction methods and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics.
Author : Phoebe A. Rice
Publisher : Royal Society of Chemistry
ISBN 13 : 0854042725
Total Pages : 417 pages
Book Rating : 4.8/5 (54 download)
Download or read book Protein-Nucleic Acid Interactions written by Phoebe A. Rice and published by Royal Society of Chemistry. This book was released on 2008-05-22 with total page 417 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides both in-depth background and up-to-date information in this area. The chapters are organized by general themes and principles, written by experts who illustrate topics with current findings. Topics covered include: - the role of ions and hydration in protein-nucleic acid interactions - transcription factors and combinatorial specificity - indirect readout of DNA sequence - single-stranded nucleic acid binding proteins - nucleic acid junctions and proteins, - RNA protein recognition - recognition of DNA damage. It will be a key reference for both advanced students and established scientists wishing to broaden their horizons.
Author : Igor F. Tsigelny
Publisher : Internat'l University Line
ISBN 13 : 9780963681775
Total Pages : 540 pages
Book Rating : 4.6/5 (817 download)
Download or read book Protein Structure Prediction written by Igor F. Tsigelny and published by Internat'l University Line. This book was released on 2002 with total page 540 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Daniel John Rigden
Publisher : Springer Science & Business Media
ISBN 13 : 1402090587
Total Pages : 330 pages
Book Rating : 4.4/5 (2 download)
Download or read book From Protein Structure to Function with Bioinformatics written by Daniel John Rigden and published by Springer Science & Business Media. This book was released on 2008-12-11 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins lie at the heart of almost all biological processes and have an incredibly wide range of activities. Central to the function of all proteins is their ability to adopt, stably or sometimes transiently, structures that allow for interaction with other molecules. An understanding of the structure of a protein can therefore lead us to a much improved picture of its molecular function. This realisation has been a prime motivation of recent Structural Genomics projects, involving large-scale experimental determination of protein structures, often those of proteins about which little is known of function. These initiatives have, in turn, stimulated the massive development of novel methods for prediction of protein function from structure. Since model structures may also take advantage of new function prediction algorithms, the first part of the book deals with the various ways in which protein structures may be predicted or inferred, including specific treatment of membrane and intrinsically disordered proteins. A detailed consideration of current structure-based function prediction methodologies forms the second part of this book, which concludes with two chapters, focusing specifically on case studies, designed to illustrate the real-world application of these methods. With bang up-to-date texts from world experts, and abundant links to publicly available resources, this book will be invaluable to anyone who studies proteins and the endlessly fascinating relationship between their structure and function.
Author : Ying Xu
Publisher : Springer Science & Business Media
ISBN 13 : 0387683720
Total Pages : 408 pages
Book Rating : 4.3/5 (876 download)
Download or read book Computational Methods for Protein Structure Prediction and Modeling written by Ying Xu and published by Springer Science & Business Media. This book was released on 2007-08-24 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Author : David Malcolm James Lilley
Publisher : Birkhauser
ISBN 13 :
Total Pages : 488 pages
Book Rating : 4.3/5 (91 download)
Download or read book Structural Tools for the Analysis of Protein-nucleic Acid Complexes written by David Malcolm James Lilley and published by Birkhauser. This book was released on 1992 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Michael J. E. Sternberg
Publisher : Oxford University Press, USA
ISBN 13 : 0191588997
Total Pages : 322 pages
Book Rating : 4.1/5 (915 download)
Download or read book Protein Structure Prediction : A Practical Approach written by Michael J. E. Sternberg and published by Oxford University Press, USA. This book was released on 1996-11-28 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional structure of proteins is a key factor in their biological activity. There is an increasing need to be able to predict the structure of a protein once its amino-acid sequence is known; this book presents practical methods of achieving that ambitious aim, using the latest computer modelling algorithms. - ;The prediction of the three-dimensional structure of a protein from its sequence is a problem faced by an ever-increasing number of biological scientists as they strive to utilize genetic information. The increasing sizes of the sequence and structural databases, the improvements in computing power, and the deeper understanding of the principles of protein structure have led to major developments in the field in the last few years. This book presents practical computer-based methods using the latest computer modelling algorithms. -
Author : Anob Mauli Chakrabarti
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (129 download)
Download or read book Integrative Computational Approaches to Study Protein-nucleic Acid Interactions written by Anob Mauli Chakrabarti and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Interactions between proteins and nucleic acid molecules are central to the cellular regulation and homeostasis. To study them, I employ a wide range of computational analysis methods to integrate genomic data from many types of experiment. This thesis has three parts. In the first part, I explore the patterns of indels created by CRISPR-Cas9 genome editing. By thorough characterisation of the precision of editing at thousands of genomic target sites, we identify simple sequence rules that can help predict these outcomes. Furthermore, we examine the role of the structural chromatin context in fine-tuning Cas9-DNA interactions. In the second part, I explore methods to study protein-RNA interactions. I use comparative computational analyses to assess both the data quality of, and data analysis methods for, different crosslinking and immunoprecipitation (CLIP) technologies. I then develop new methods to analyse data generated by hybrid individual-nucleotide resolution CLIP (hiCLIP). By tailoring computational solutions to an understanding of experimental conditions, I improve the overall sensitivity of hiCLIP, and ultimately feedback to drive ongoing experimental development. In the third part, I focus on the Staufen family of double-stranded RNA binding proteins and using hiCLIP data to define transcriptome-wide atlases of RNA duplexes bound by these proteins both in a cell line and in rat brain tissue. Through integration with other data sets, both publicly available and newly generated, I derive insights into their function in RNA metabolism, and in how these interactions change during the course of mammalian brain development with putative roles in ribonucleoprotein complex formation. In summary, I present a range of tailored computational methods and analyses developed to understand interactions between proteins and nucleic acids; aiming to link these interactions to functional outcomes.
Author : Huzefa Rangwala
Publisher : John Wiley & Sons
ISBN 13 : 111809946X
Total Pages : 611 pages
Book Rating : 4.1/5 (18 download)
Download or read book Introduction to Protein Structure Prediction written by Huzefa Rangwala and published by John Wiley & Sons. This book was released on 2011-03-16 with total page 611 pages. Available in PDF, EPUB and Kindle. Book excerpt: A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the modeled structures The computational model that detects the differences between protein structure and its modeled mutant Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.
Author :
Publisher :
ISBN 13 :
Total Pages : 886 pages
Book Rating : 4.F/5 ( download)
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2008 with total page 886 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : David Webster
Publisher : Springer Science & Business Media
ISBN 13 : 1592593682
Total Pages : 425 pages
Book Rating : 4.5/5 (925 download)
Download or read book Protein Structure Prediction written by David Webster and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: The number of protein sequences grows each year, yet the number of structures deposited in the Protein Data Bank remains relatively small. The importance of protein structure prediction cannot be overemphasized, and this volume is a timely addition to the literature in this field. Protein Structure Prediction: Methods and Protocols is a departure from the normal Methods in Molecular Biology series format. By its very nature, protein structure prediction demands that there be a greater mix of theoretical and practical aspects than is normally seen in this series. This book is aimed at both the novice and the experienced researcher who wish for detailed inf- mation in the field of protein structure prediction; a major intention here is to include important information that is needed in the day-to-day work of a research scientist, important information that is not always decipherable in scientific literature. Protein Structure Prediction: Methods and Protocols covers the topic of protein structure prediction in an eclectic fashion, detailing aspects of pred- tion that range from sequence analysis (a starting point for many algorithms) to secondary and tertiary methods, on into the prediction of docked complexes (an essential point in order to fully understand biological function). As this volume progresses, the authors contribute their expert knowledge of protein structure prediction to many disciplines, such as the identification of motifs and domains, the comparative modeling of proteins, and ab initio approaches to protein loop, side chain, and protein prediction.
Author : Melina Z. Bayramyan
Publisher :
ISBN 13 :
Total Pages : 680 pages
Book Rating : 4.:/5 (651 download)
Download or read book Computational Analysis and Modeling of Protein-RNA Complexes and Nucleic Acid Structure written by Melina Z. Bayramyan and published by . This book was released on 2005 with total page 680 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Concettina Guerra
Publisher : Springer Science & Business Media
ISBN 13 : 3540401040
Total Pages : 161 pages
Book Rating : 4.5/5 (44 download)
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.
