Download or read book Data Analytics for Protein Crystallization written by Marc L. Pusey and published by Springer. This book was released on 2017-11-27 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique text/reference presents an overview of the computational aspects of protein crystallization, describing how to build robotic high-throughput and crystallization analysis systems. The coverage encompasses the complete data analysis cycle, including the set-up of screens by analyzing prior crystallization trials, the classification of crystallization trial images by effective feature extraction, the analysis of crystal growth in time series images, the segmentation of crystal regions in images, the application of focal stacking methods for crystallization images, and the visualization of trials. Topics and features: describes the fundamentals of protein crystallization, and the scoring and categorization of crystallization image trials; introduces a selection of computational methods for protein crystallization screening, and the hardware and software architecture for a basic high-throughput system; presents an overview of the image features used in protein crystallization classification, and a spatio-temporal analysis of protein crystal growth; examines focal stacking techniques to avoid blurred crystallization images, and different thresholding methods for binarization or segmentation; discusses visualization methods and software for protein crystallization analysis, and reviews alternative methods to X-ray diffraction for obtaining structural information; provides an overview of the current challenges and potential future trends in protein crystallization. This interdisciplinary work serves as an essential reference on the computational and data analytics components of protein crystallization for the structural biology community, in addition to computer scientists wishing to enter the field of protein crystallization.
Download or read book Protein Crystallization Strategies for Structural Genomics written by Naomi E. Chayen and published by Internat'l University Line. This book was released on 2007 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Crystallization written by Terese M. Bergfors and published by Internat'l University Line. This book was released on 2009 with total page 505 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Crystallography written by Gwyndaf Evans and published by Royal Society of Chemistry. This book was released on 2018-06-21 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein crystallography has become vital to further understanding the structure and function of many complex biological systems. In recent years, structure determination has progressed tremendously however the quality of crystals and data sets can prevent the best results from being obtained. With contributions from world leading researchers whose software are used worldwide, this book provides a coherent approach on how to handle difficult crystallographic data and how to assess its quality. The chapters will cover all key aspects of protein crystallography, from instrumentation and data processing through to model building. This book also addresses challenges that protein crystallographers will face such as dealing with data from microcrystals and multi protein complexes. This book is ideal for both academics and researchers in industry looking for a comprehensive guide to protein crystallography.
Download or read book Preparation and Analysis of Protein Crystals written by Alexander McPherson and published by John Wiley & Sons. This book was released on 1982-05-04 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: A complete guide to techniques and procedures for the preparation of proteins for crystallographic studies. Describes methods for protein crystallization; formation of isomorphous heavy atoms; x-ray diffraction and analysis; and photographic and computerbased data collection methods and instrumentation.
Download or read book The Next Generation in Membrane Protein Structure Determination written by Isabel Moraes and published by Springer. This book was released on 2016-08-23 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews current techniques used in membrane protein structural biology, with a strong focus on practical issues. The study of membrane protein structures not only provides a basic understanding of life at the molecular level but also helps in the rational and targeted design of new drugs with reduced side effects. Today, about 60% of the commercially available drugs target membrane proteins and it is estimated that nearly 30% of proteins encoded in the human genome are membrane proteins. In recent years much effort has been put towards innovative developments to overcome the numerous obstacles associated with the structure determination of membrane proteins. This book reviews a variety of recent techniques that are essential to any modern researcher in the field of membrane protein structural biology. The topics that are discussed are not commonly found in textbooks. The scope of this book includes: Expression screening using fluorescent proteins The use of detergents in membrane protein research The use of NMR Synchrotron developments in membrane protein structural biology Visualisation and X-ray data collection of microcrystals X-ray diffraction data analysis from multiple crystals Serial millisecond crystallography Serial femtosecond crystallography Membrane protein structures in drug discovery The information provided in this book should be of interest to anyone working in the area of structural biology. Students will find carefully prepared overviews of basic ideas and advanced protein scientists will find the level of detail required to apply the material directly to their day to day work. Chapters 4, 5, 6, 8 and 9 of this book are published open access under a CC BY 4.0 license at link.springer.com.
Download or read book Crystals X rays and Proteins written by Dennis Sherwood and published by OUP Oxford. This book was released on 2010-11-05 with total page 644 pages. Available in PDF, EPUB and Kindle. Book excerpt: A complete account of the theory of the diffraction of X-rays by crystals, with particular reference to the processes of determining the structures of protein molecules. This book is aimed primarily at structural biologists and biochemists but will also be valuable to those entering the field with a background in physical sciences or chemistry. It may be used at any post-school level, and develops from first principles all relevant mathematics, diffraction and wave theory, assuming no mathematical knowledge beyond integral calculus. The book covers a host of important topics in the area, including: - The practical aspects of sample preparation and X-ray data collection, using both laboratory and synchrotron sources - Data analysis at both theoretical and practical levels - The important role played by the Patterson function in structure analysis, by both molecular replacement and experimental phasing approaches - Methods for improving the resulting electron density map - The theoretical basis of methods used in refinement of protein crystal structures - In-depth explanation of the crucial task of defining the binding sites of ligands and drug molecules - The complementary roles of other diffraction methods: these reveal further detail of great functional importance in a crystal structure.
Download or read book Computational Support Systems for Prediction and Characterization of Protein Crystallization Outcomes written by Marcin Jerzy Mizianty and published by . This book was released on 2013 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt: Analysis of protein structures may reveal their function, regulation and interactions. Almost 90% of the known protein structures were solved using X-ray crystallography; however, many more structures remain unsolved. Protein Structure Initiative (PSI) project was created to speed up structure determination. PSI includes structural genomics (SG) centers that perform high-throughput crystallization which processes hundreds of proteins using standardized protocols. Large quantities of crystallization data generated by PSI fueled research that looked into proteins' properties associated with success of crystallization. In spite of intense research crystallization of proteins is still among the most complex and least understood problems in structural biology. Since SG centers do not focus on individual proteins, but rather on covering the protein structure space, they have certain flexibility in selection of targets. At the beginning of my PhD program we designed and assessed three accurate methods that predict crystallization propensity based on a protein sequence. These methods could be used to prioritize targets based on their predicted propensity for the successful structure determination. We observed that as the crystallization protocols are updated the predictors of crystallization propensity need to be correspondingly upgraded and enhanced. To this end, in the course of the thesis we developed an accurate predictor that generates crystallization propensity and indicates causes of the potential crystallization failure, which can occur at any of the three major steps in the protein crystallization protocol: production of protein material, purification, and production of crystals. Our predictors are empirically compared against state-of-the-art in the field demonstrating favorable predictive performance. Finally, we designed another accurate and runtime-efficient method which we then used to perform first-of-its-kind large-scale analysis of crystallization propensity for proteins encoded in 1,953 fully sequenced genomes. Analysis of these predictions shows that current X-ray crystallography combined with homology modeling could provide an average per-proteome structural coverage of 73% with over 60% coverage for archaea and bacterial proteomes, and between 35 and 70% for eukaryotes. Moreover, our study revealed that use of knowledge-based target selection increases coverage by a significant margin, which for majority of organisms is between 25 to 40%.
Download or read book Preparation and Analysis of Protein Crystals written by Alexander McPherson and published by . This book was released on 1989 with total page 371 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Membrane Protein Crystallization written by and published by Academic Press. This book was released on 2009-05-29 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume of Current Topics in Membranes focuses on Membrane Protein Crystallization, beginning with a review of past successes and general trends, then further discussing challenges of mebranes protein crystallization, cell free production of membrane proteins and novel lipids for membrane protein crystallization. This publication also includes tools to enchance membrane protein crystallization, technique advancements, and crystallization strategies used for photosystem I and its complexes, establishing Membrane Protein Crystallization as a needed, practical reference for researchers.
Download or read book Knowledge Discovery in Proteomics written by Igor Jurisica and published by CRC Press. This book was released on 2005-09-02 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Multi-modal representations, the lack of complete and consistent domain theories, rapid evolution of domain knowledge, high dimensionality, and large amounts of missing information - these are challenges inherent in modern proteomics. As our understanding of protein structure and function becomes ever more complicated, we have reached a point where
Download or read book Biomolecular Crystallography written by Bernhard Rupp and published by Garland Science. This book was released on 2009-10-20 with total page 832 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthesizing over thirty years of advances into a comprehensive textbook, Biomolecular Crystallography describes the fundamentals, practices, and applications of protein crystallography. Illustrated in full-color by the author, the text describes mathematical and physical concepts in accessible and accurate language. Biomolecular Crystallography will be a valuable resource for advanced undergraduate and graduate students and practitioners in structural biology, crystallography, and structural bioinformatics.
Download or read book Practical Protein Crystallography written by Duncan E. McRee and published by Academic Press. This book was released on 2012-12-02 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: Designed for easy use by both new and experienced protein crystallographers, this much-needed book is for anyone interested in solving protein structures by the method of crystallography. It contains many examples ofactual experiments and data, including electron density maps. Computer methods and computer code samples are presented. Practical Protein Crystallography is loaded with new information on area detectors, synchrotron radiation techniques, and the latest computer methods, and features the XtalView software system. Graduate students and teachers in physical biochemistry and pharmaceutical researchers will find this text a timely and convenient aid.
Download or read book Membrane Protein Purification and Crystallization written by Carola Hunte and published by Elsevier. This book was released on 2003-01-05 with total page 339 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition of Membrane Protein Purification and Crystallization, A Practical Guide is written for bench scientists working in the fields of biochemistry, biology, and proteomic research. This guide presents isolation and crystallization techniques in a concise form, emphasizing the critical aspects unique to membrane proteins. It explains the principles of the methods and provides protocols of general use, permitting researchers and students new to this area to adapt these techniques to their particular needs. This edition is not only an update but is comprised mainly of new contributions. It is the first monograph compiling the essential approaches for membrane protein crystallization, and emphasizes recent progress in production and purification of recombinant membrane proteins. Provides general guidelines and strategies for isolation and crystallization of membrane proteins Gives detailed protocols that have wide application, and low specialized equipment needs Emphasizes recent progress in production and purification of recombinant membrane proteins, especially of histidine-tagged and other affinity-epitope-tagged proteins Summarizes recent developments of Blue-Native PAGE, a high resolution separation technique, which is independent of the use of recombinant techniques, and is especially suited for proteomic analyses of membrane protein complexes Gives detailed protocols for membrane protein crystallization, and describes the production and use of antibody fragments for high resolution crystallization Presents a comprehensive guide to 2D-crystallization of membrane proteins
Download or read book Data Mining for Protein Structure Analysis and Crystallization Trials Using Physical Chemical Constrains written by Dmitrii Arkadyevich Polshakov and published by . This book was released on 2005 with total page 110 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Crystallization of Membrane Proteins written by Hartmut Michel and published by CRC Press. This book was released on 2018-01-18 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: The precise knowledge of the structure of biological macromolecules forms the basis of understanding their function and their mechanism of action. It also lays the foundation for rational protein and drug design. The only method to obtain this knowledge is still crystallography. At present, the structures of about 400 proteins are known at or nearly at atomic proteins. However, only two of them are membrane proteins or complexes of the membrane proteins. The reasons for the difference is not the crystals of membrane proteins resists forming special problems when being analysed. The reason is that the membrane proteins resist into forming into well-ordered crystals. The intention of this book is to help to produce well-ordered crystals proteins and to provide guidelines, it is aimed at both biochemists and protein crystallographer‘s.
Download or read book Scalable Big Data Analytics for Protein Bioinformatics written by Dariusz Mrozek and published by Springer. This book was released on 2018-09-25 with total page 315 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a focus on proteins and their structures. The text describes various scalable solutions for protein structure similarity searching, carried out at main representation levels and for prediction of 3D structures of proteins. Emphasis is placed on techniques that can be used to accelerate similarity searches and protein structure modeling processes. The content of the book is divided into four parts. The first part provides background information on proteins and their representation levels, including a formal model of a 3D protein structure used in computational processes, and a brief overview of the technologies used in the solutions presented in the book. The second part of the book discusses Cloud services that are utilized in the development of scalable and reliable cloud applications for 3D protein structure similarity searching and protein structure prediction. The third part of the book shows the utilization of scalable Big Data computational frameworks, like Hadoop and Spark, in massive 3D protein structure alignments and identification of intrinsically disordered regions in protein structures. The fourth part of the book focuses on finding 3D protein structure similarities, accelerated with the use of GPUs and the use of multithreading and relational databases for efficient approximate searching on protein secondary structures. The book introduces advanced techniques and computational architectures that benefit from recent achievements in the field of computing and parallelism. Recent developments in computer science have allowed algorithms previously considered too time-consuming to now be efficiently used for applications in bioinformatics and the life sciences. Given its depth of coverage, the book will be of interest to researchers and software developers working in the fields of structural bioinformatics and biomedical databases.
