Hybrid Biomolecular Modeling
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| Author | : Slavica Jonic |
| Publisher | : Frontiers Media SA |
| Total Pages | : 128 |
| Release | : 2019-01-24 |
| Genre | : |
| ISBN | : 2889456994 |
Models of biomolecular structure and dynamics are often obtained by combining simulation or prediction approaches (e.g., comparative modeling, Molecular Dynamics (MD) simulations, Normal Mode Analysis (NMA), etc.) with experimental approaches (e.g., Nuclear Magnetic Resonance (NMR), X-ray crystallography, Small-Angle X-ray Scattering (SAXS), Electron Microscopy (EM), etc.). Such hybrid modeling extends the capabilities of experimental techniques, by enriching structural information and facilitating dynamics studies of biomolecules. This eBook contains articles on methodological developments, applications, and challenges of hybrid biomolecular modeling that have been collected in the framework of the Frontiers Research Topic entitled “Hybrid Biomolecular Modeling”.
| Author | : Andrei L. Tchougréeff |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 360 |
| Release | : 2008-08-01 |
| Genre | : Science |
| ISBN | : 1402081898 |
This is a self-contained advanced review offering step by step derivation of the consistent theoretical picture of hybrid modeling methods and the thorough analysis of the concepts and current practical methods of hybrid modeling based on this theory. The book presents its material in a sequential way paying attention both to the physical soundness of the approximations used and to the mathematical rigor necessary for practical developing of the robust modeling code.
| Author | : Martin J. Field |
| Publisher | : Cambridge University Press |
| Total Pages | : 294 |
| Release | : 2007-07-19 |
| Genre | : Science |
| ISBN | : 1139465813 |
Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.
| Author | : Valentina Tozzini |
| Publisher | : Frontiers Media SA |
| Total Pages | : 235 |
| Release | : 2020-10-27 |
| Genre | : Science |
| ISBN | : 2889661091 |
This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
| Author | : Haruki Nakamura |
| Publisher | : Springer |
| Total Pages | : 272 |
| Release | : 2019-01-08 |
| Genre | : Science |
| ISBN | : 9811322007 |
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.
| Author | : Michael S. Lee |
| Publisher | : |
| Total Pages | : 18 |
| Release | : 2004 |
| Genre | : Molecular biology |
| ISBN | : |
In this work, we design and use a new biomolecular simulation technique that combines explicit solvent molecules and implicit solvent theory. We employ a multigrid approach to speed up the computationally expensive long-range electrostatic energy terms ubiquitous to the classical simulation of biomolecules. It is shown that the multigrid technique affords an order-of-magnitude speedup over conventional cutoff approaches. Our algorithm makes possible a new class of biomolecular simulations that was previously untenable (i.e., the calculation of solvation energies of entire proteins using explicit water molecules). We present comparisons of protein solvation energies obtained from our method and a popular implicit solvent model.
| Author | : Alan Hinchliffe |
| Publisher | : Wiley-Blackwell |
| Total Pages | : 440 |
| Release | : 2008-11-17 |
| Genre | : Medical |
| ISBN | : |
Updated to appeal to today's student, 'Molecular Modeling for Beginners', provides a concise, basic introduction to this evolving and developing field. It includes many real chemical applications combined with worked problems and solutions in each chapter.
| Author | : Qiong Cai |
| Publisher | : |
| Total Pages | : |
| Release | : 2007 |
| Genre | : |
| ISBN | : |
| Author | : Tamar Schlick |
| Publisher | : Royal Society of Chemistry |
| Total Pages | : 381 |
| Release | : 2012-05-24 |
| Genre | : Science |
| ISBN | : 1849735042 |
The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.
| Author | : Hans-Dieter Höltje |
| Publisher | : John Wiley & Sons |
| Total Pages | : 206 |
| Release | : 2008-07-11 |
| Genre | : Science |
| ISBN | : 3527614761 |
Written by experienced experts in molecular modeling, this books describes the basics to the extent that is necessary if one wants to be able to reliably judge the results from molecular modeling calculations. Its main objective is the description of the various pitfalls to be avoided. Without unnecessary overhead it leads the reader from simple calculations on small molecules to the modeling of proteins and other relevant biomolecules. A textbook for beginners as well as an invaluable reference for all those dealing with molecular modeling in their daily work!
