Implicit Solvent Method Development And Application PDF Download
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| Author | : John Thomas Mongan |
| Publisher | : |
| Total Pages | : 163 |
| Release | : 2006 |
| Genre | : |
| ISBN | : |
Download Implicit Solvent Method Development and Application Book in PDF, ePub and Kindle
Implicit solvation provides a means of accelerating and improving the efficiency of computational biomolecular studies by eliminating explicit solvent degrees of freedom while still representing the effects of solvation. Evidence is provided supporting the importance of defining the implicit solvent-solute boundary such that solvent is excluded from spaces smaller than a water molecule. The pairwise analytical generalized Born (GB) model, a popular implicit solvent model, is extended to incorporate this property. Methods for conducting molecular dynamics simulations at a constant pH, rather than the traditional constant protonation state, are reviewed and a constant pH method employing a consistent GB-based Hamiltonian for conformational and protonation state sampling is developed. Even with the improved efficiency of implicit solvent, it is difficult to achieve sufficient sampling in molecular dynamics. This problem is addressed by accelerated molecular dynamics, a technique for accelerating sampling that requires no advance knowledge of the potential energy landscape is presented. Analysis of molecular dynamics data is aided by Interactive Essential Dynamics, a tool for visualization of principal component analysis results. Implicit solvent methods are applied to the computer-aided design of inhibitors for the zinc(II) proteases stromelysin-1 and anthrax lethal factor. Inhibitors with IC-50 of 100 nM and 14 micromolar are reported for stromelysin-1 and lethal factor, respectively. Use of the GB model developed here allows for accurate elucidation of the binding mode of the lethal factor inhibitor, while GB models that allow solvent in spaces smaller than a water molecule identify an incorrect binding mode.
| Author | : Ralph A. Wheeler |
| Publisher | : Elsevier |
| Total Pages | : 271 |
| Release | : 2008-10-30 |
| Genre | : Science |
| ISBN | : 0080932789 |
Download Annual Reports in Computational Chemistry Book in PDF, ePub and Kindle
Annual Reports in Computational Chemistry is a new periodical providing timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Each volume is organized into (thematic) sections with contributions written by experts. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. Annual Reports in Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry. * Broad coverage of computational chemistry and up-to-date information * Topics covered include bioinformatics, drug discovery, protein NMR, simulation methodologies, and applications in academic and industrial settings * Each chapter reviews the most recent literature on a specific topic of interest to computational chemists
| Author | : Hatem Hamdi Ahmed Helal |
| Publisher | : |
| Total Pages | : |
| Release | : 2011 |
| Genre | : |
| ISBN | : |
Download Including Solvent Effects in First-principles Simulations of Biological Systems Book in PDF, ePub and Kindle
| Author | : Kunal Roy |
| Publisher | : Elsevier |
| Total Pages | : 768 |
| Release | : 2023-05-23 |
| Genre | : Medical |
| ISBN | : 0443186391 |
Download Cheminformatics, QSAR and Machine Learning Applications for Novel Drug Development Book in PDF, ePub and Kindle
Cheminformatics, QSAR and Machine Learning Applications for Novel Drug Development aims at showcasing different structure-based, ligand-based, and machine learning tools currently used in drug design. It also highlights special topics of computational drug design together with the available tools and databases. The integrated presentation of chemometrics, cheminformatics, and machine learning methods under is one of the strengths of the book.The first part of the content is devoted to establishing the foundations of the area. Here recent trends in computational modeling of drugs are presented. Other topics present in this part include QSAR in medicinal chemistry, structure-based methods, chemoinformatics and chemometric approaches, and machine learning methods in drug design. The second part focuses on methods and case studies including molecular descriptors, molecular similarity, structure-based based screening, homology modeling in protein structure predictions, molecular docking, stability of drug receptor interactions, deep learning and support vector machine in drug design. The third part of the book is dedicated to special topics, including dedicated chapters on topics ranging from de design of green pharmaceuticals to computational toxicology. The final part is dedicated to present the available tools and databases, including QSAR databases, free tools and databases in ligand and structure-based drug design, and machine learning resources for drug design. The final chapters discuss different web servers used for identification of various drug candidates. Presents chemometrics, cheminformatics and machine learning methods under a single reference Showcases the different structure-based, ligand-based and machine learning tools currently used in drug design Highlights special topics of computational drug design and available tools and databases
| Author | : Sean Ekins |
| Publisher | : John Wiley & Sons |
| Total Pages | : 840 |
| Release | : 2006-07-11 |
| Genre | : Medical |
| ISBN | : 0470037229 |
Download Computer Applications in Pharmaceutical Research and Development Book in PDF, ePub and Kindle
A unique, holistic approach covering all functions and phases of pharmaceutical research and development While there are a number of texts dedicated to individual aspects of pharmaceutical research and development, this unique contributed work takes a holistic and integrative approach to the use of computers in all phases of drug discovery, development, and marketing. It explains how applications are used at various stages, including bioinformatics, data mining, predicting human response to drugs, and high-throughput screening. By providing a comprehensive view, the book offers readers a unique framework and systems perspective from which they can devise strategies to thoroughly exploit the use of computers in their organizations during all phases of the discovery and development process. Chapters are organized into the following sections: * Computers in pharmaceutical research and development: a general overview * Understanding diseases: mining complex systems for knowledge * Scientific information handling and enhancing productivity * Computers in drug discovery * Computers in preclinical development * Computers in development decision making, economics, and market analysis * Computers in clinical development * Future applications and future development Each chapter is written by one or more leading experts in the field and carefully edited to ensure a consistent structure and approach throughout the book. Figures are used extensively to illustrate complex concepts and multifaceted processes. References are provided in each chapter to enable readers to continue investigating a particular topic in depth. Finally, tables of software resources are provided in many of the chapters. This is essential reading for IT professionals and scientists in the pharmaceutical industry as well as researchers involved in informatics and ADMET, drug discovery, and technology development. The book's cross-functional, all-phases approach provides a unique opportunity for a holistic analysis and assessment of computer applications in pharmaceutics.
| Author | : Darrin M. York |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 426 |
| Release | : 2009-05-30 |
| Genre | : Science |
| ISBN | : 1402099568 |
Download Multi-scale Quantum Models for Biocatalysis Book in PDF, ePub and Kindle
“Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes. This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.
| Author | : Slavica Jonic |
| Publisher | : Frontiers Media SA |
| Total Pages | : 128 |
| Release | : 2019-01-24 |
| Genre | : |
| ISBN | : 2889456994 |
Download Hybrid Biomolecular Modeling Book in PDF, ePub and Kindle
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 | : Jianzhong Wu |
| Publisher | : Springer |
| Total Pages | : 331 |
| Release | : 2016-12-17 |
| Genre | : Science |
| ISBN | : 9811025029 |
Download Variational Methods in Molecular Modeling Book in PDF, ePub and Kindle
This book presents tutorial overviews for many applications of variational methods to molecular modeling. Topics discussed include the Gibbs-Bogoliubov-Feynman variational principle, square-gradient models, classical density functional theories, self-consistent-field theories, phase-field methods, Ginzburg-Landau and Helfrich-type phenomenological models, dynamical density functional theory, and variational Monte Carlo methods. Illustrative examples are given to facilitate understanding of the basic concepts and quantitative prediction of the properties and rich behavior of diverse many-body systems ranging from inhomogeneous fluids, electrolytes and ionic liquids in micropores, colloidal dispersions, liquid crystals, polymer blends, lipid membranes, microemulsions, magnetic materials and high-temperature superconductors. All chapters are written by leading experts in the field and illustrated with tutorial examples for their practical applications to specific subjects. With emphasis placed on physical understanding rather than on rigorous mathematical derivations, the content is accessible to graduate students and researchers in the broad areas of materials science and engineering, chemistry, chemical and biomolecular engineering, applied mathematics, condensed-matter physics, without specific training in theoretical physics or calculus of variations.
| Author | : Michael Feig |
| Publisher | : John Wiley & Sons |
| Total Pages | : 334 |
| Release | : 2009-12-09 |
| Genre | : Science |
| ISBN | : 3527629262 |
Download Modeling Solvent Environments Book in PDF, ePub and Kindle
A comprehensive view of the current methods for modeling solvent environments with contributions from the leading researchers in the field. Throughout, the emphasis is placed on the application of such models in simulation studies of biological processes, although the coverage is sufficiently broad to extend to other systems as well. As such, this monograph treats a full range of topics, from statistical mechanics-based approaches to popular mean field formalisms, coarse-grained solvent models, more established explicit, fully atomic solvent models, and recent advances in applying ab initio methods for modeling solvent properties.
| Author | : David A. Puleo |
| Publisher | : Springer Science & Business Media |
| Total Pages | : 438 |
| Release | : 2009-06-26 |
| Genre | : Technology & Engineering |
| ISBN | : 0387981616 |
Download Biological Interactions on Materials Surfaces Book in PDF, ePub and Kindle
Success or failure of biomaterials, whether tissue engineered constructs, joint and dental implants, vascular grafts, or heart valves, depends on molecular-level events that determine subsequent responses of cells and tissues. This book presents the latest developments and state-of-the-art knowledge regarding protein, cell, and tissue interactions with both conventional and nanophase materials. Insight into these biomaterial surface interactions will play a critical role in further developments in fields such as tissue engineering, regenerative medicine, and biocompatibility of implanted materials and devices. With chapters written by leaders in their respective fields, this compendium will be the authoritative source of information for scientists, engineers, and medical researchers seeking not only to understand but also to control tissue-biomaterial interactions.
