Download or read book Computational modelling in structural biology insights from small angel scattering and molecular dynamics simulations written by and published by . This book was released on with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Scattering Methods in Structural Biology Part B written by and published by Elsevier. This book was released on 2023-01-12 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scattering Methods in Structural Biology, Part B, Volume 676 in the Methods in Enzymology serial, highlights advances in the field, presenting chapters on Quality controls, Refining biomolecular structures and ensembles by SAXS-driven molecular dynamics simulations, Data analysis and modelling of small-angle scattering data with contrast variation, Observing protein degradation in solution by the PAN-20S proteasome complex: state-of-the-art and future perspectives of TR-SANS as a complementary tool to NMR, crystallography and Cryo-EM, Extracting structural insights from chemically-specific soft X-ray scattering, Reconstruction of 3D density of biological macromolecules from solution scattering, ATSAS- present state and new developments in computational methods, and much more. Additional chapters cover Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles (FoXSDock and MultiFoXS), Validation of macromolecular flexibility in solution by SAXS, Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes, Application of Molecular Simulation Methods to Analyze SAS Data, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology serial Updated release includes the latest information on Small Angle Scattering Methods for Structural Interpretation

Download or read book Scattering Methods in Structural Biology Part B written by and published by Elsevier. This book was released on 2023-01-20 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scattering Methods in Structural Biology, Part B, Volume 676 in the Methods in Enzymology serial, highlights advances in the field, presenting chapters on Quality controls, Refining biomolecular structures and ensembles by SAXS-driven molecular dynamics simulations, Data analysis and modelling of small-angle scattering data with contrast variation, Observing protein degradation in solution by the PAN-20S proteasome complex: state-of-the-art and future perspectives of TR-SANS as a complementary tool to NMR, crystallography and Cryo-EM, Extracting structural insights from chemically-specific soft X-ray scattering, Reconstruction of 3D density of biological macromolecules from solution scattering, ATSAS- present state and new developments in computational methods, and much more. Additional chapters cover Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles (FoXSDock and MultiFoXS), Validation of macromolecular flexibility in solution by SAXS, Combining NMR, SAXS and SANS to characterize the structure and dynamics of protein complexes, Application of Molecular Simulation Methods to Analyze SAS Data, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology serial Updated release includes the latest information on Small Angle Scattering Methods for Structural Interpretation

Download or read book Integrative Structural Biology with Hybrid Methods written by Haruki Nakamura and published by Springer. This book was released on 2019-01-08 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.

Download or read book Lecture Notes on Computational Structural Biology written by Zhijun Wu and published by World Scientific. This book was released on 2008 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt: 1. Introduction. 1.1. Protein structure. 1.2. Structure determination. 1.3. Dynamics simulation. 1.4. The myth of protein folding -- 2. X-ray crystallography computing. 2.1. The phase problem. 2.2. Least squares solutions. 2.3. Entropy maximization. 2.4. Indirect methods -- 3. NMR structure determination. 3.1. Nuclear magnetic resonance. 3.2. Distance geometry. 3.3. Distance-based modeling. 3.4. Structural analysis -- 4. Potential energy minimization. 4.1. Potential energy function. 4.2. Local optimization. 4.3. Global optimization. 4.4. Energy transformation -- 5. Molecular dynamics simulation. 5.1. Equations of motion. 5.2. Initial-value problem. 5.3. Boundary-value problem. 5.4. Normal mode analysis -- 6. Knowledge-based protein modeling. 6.1. Sequence/structural alignment. 6.2. Fold recognition/inverse folding. 6.3. Knowledge-based structural refinement. 6.4. Structural computing and beyond

Download or read book Computational Structural Biology written by Manuel Claude Peitsch and published by World Scientific. This book was released on 2008 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: This work covers the impact of computational structural biology on protein structure prediction methods, macromolecular function and protein design, and key methods in drug discovery. It also addresses the computational challenges of experimental approaches in structural biology.

Download or read book Advances in Protein Molecular and Structural Biology Methods written by Timir Tripathi and published by Academic Press. This book was released on 2022-01-14 with total page 716 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Download or read book Small Angle Scattering Part A Methods for Structural Investigation written by and published by Academic Press. This book was released on 2022-11-19 with total page 578 pages. Available in PDF, EPUB and Kindle. Book excerpt: Small Angle Scattering, Part A: Methods for Structural Investigation, Volume 675 in the Methods in Enzymology series, highlights new advances in the field, with new chapters in this updated release including SAXS foundations and metrics, Contrast variation sample preparation protocols, experimental procedures, and rudimentary analysis, Molecular deuteration for neutron scattering, Planning, Executing and Assessing the Feasibility of SANS Contrast Variation Experiments, Technical considerations for small-angle neutron scattering from biological macromolecules, and Advanced sample environments and capabilities at our synchrotron X-ray beamline with example applications. Additional sections in the book cover SEC-SAXS-MALS data acquisition and processing pipeline at SIBYLS, SEC-SAXS: pros and cons, experimental set-up, examples and software developments, Radiation damage and sample economy for stopped-flow methods in the time regime of millisecond and above, Stopped-flow-time-resolved SAXS, Insights on Temp-jump, time-resolved SAXS, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Includes the latest information on Small Angle Scattering: Methods for Structural Investigation

Download or read book Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design written by Sanjeev Kumar Singh and published by Springer Nature. This book was released on 2021-02-02 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.

Download or read book Computational Biochemistry and Biophysics written by Oren M. Becker and published by CRC Press. This book was released on 2001-02-09 with total page 525 pages. Available in PDF, EPUB and Kindle. Book excerpt: Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret biomolecular properties gleaned from computer-generated membrane simulations. It also demonstrates comparative protein structure modeling, outlines computer-aided drug design, discusses Bayesian statistics in molecular and structural biology, and examines the RISM-SCF/MCSCF approach to chemical processes in solution.

Download or read book Biological Small Angle Scattering Techniques Strategies and Tips written by Barnali Chaudhuri and published by Springer. This book was released on 2017-12-07 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a clear, comprehensible and up-to-date description of how Small Angle Scattering (SAS) can help structural biology researchers. SAS is an efficient technique that offers structural information on how biological macromolecules behave in solution. SAS provides distinct and complementary data for integrative structural biology approaches in combination with other widely used probes, such as X-ray crystallography, Nuclear magnetic resonance, Mass spectrometry and Cryo-electron Microscopy. The development of brilliant synchrotron small-angle X-ray scattering (SAXS) beam lines has increased the number of researchers interested in solution scattering. SAS is especially useful for studying conformational changes in proteins, highly flexible proteins, and intrinsically disordered proteins. Small-angle neutron scattering (SANS) with neutron contrast variation is ideally suited for studying multi-component assemblies as well as membrane proteins that are stabilized in surfactant micelles or vesicles. SAS is also used for studying dynamic processes of protein fibrillation in amyloid diseases, and pharmaceutical drug delivery. The combination with size-exclusion chromatography further increases the range of SAS applications. The book is written by leading experts in solution SAS methodologies. The principles and theoretical background of various SAS techniques are included, along with practical aspects that range from sample preparation to data presentation for publication. Topics covered include techniques for improving data quality and analysis, as well as different scientific applications of SAS. With abundant illustrations and practical tips, we hope the clear explanations of the principles and the reviews on the latest progresses will serve as a guide through all aspects of biological solution SAS. The scope of this book is particularly relevant for structural biology researchers who are new to SAS. Advanced users of the technique will find it helpful for exploring the diversity of solution SAS methods and applications. Chapter 3 of this book is available open access under a CC BY 4.0 license at link.springer.com.

Download or read book Monoclonal Antibodies written by Christian Klein and published by MDPI. This book was released on 2018-04-27 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a printed edition of the Special Issue "Monoclonal Antibodies" that was published in Antibodies

Download or read book Experiments and Simulations A Pas de Deux to Unravel Biological Function written by Massimiliano Bonomi and published by Frontiers Media SA. This book was released on 2022-01-19 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Biology and Applied Bioinformatics written by Heitor Lopes and published by BoD – Books on Demand. This book was released on 2011-09-02 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nowadays it is difficult to imagine an area of knowledge that can continue developing without the use of computers and informatics. It is not different with biology, that has seen an unpredictable growth in recent decades, with the rise of a new discipline, bioinformatics, bringing together molecular biology, biotechnology and information technology. More recently, the development of high throughput techniques, such as microarray, mass spectrometry and DNA sequencing, has increased the need of computational support to collect, store, retrieve, analyze, and correlate huge data sets of complex information. On the other hand, the growth of the computational power for processing and storage has also increased the necessity for deeper knowledge in the field. The development of bioinformatics has allowed now the emergence of systems biology, the study of the interactions between the components of a biological system, and how these interactions give rise to the function and behavior of a living being. This book presents some theoretical issues, reviews, and a variety of bioinformatics applications. For better understanding, the chapters were grouped in two parts. In Part I, the chapters are more oriented towards literature review and theoretical issues. Part II consists of application-oriented chapters that report case studies in which a specific biological problem is treated with bioinformatics tools.

Download or read book Computational Structural Biology written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer Science & Business Media. This book was released on 2013-07-17 with total page 809 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.

Download or read book Multiscale Approaches to Protein Modeling written by Andrzej Kolinski and published by Springer Science & Business Media. This book was released on 2010-10-13 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.