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Author: Publisher: ISBN: Category : Molecular biology Languages : en Pages : 18
Book Description
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: Publisher: ISBN: Category : Molecular biology Languages : en Pages : 18
Book Description
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: Michael S. Lee Publisher: ISBN: Category : Molecular biology Languages : en Pages : 18
Book Description
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: Publisher: ISBN: Category : Languages : en Pages : 13
Book Description
We present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid method for evaluating the pairwise electrostatic and GB terms. It is shown that for typical ion and protein simulations our method achieves similar equilibrium and dynamical observables as the conventional particle mesh Ewald (PME) method. Simulation timings are reported, which indicate that the hybrid method is much faster than PME, primarily due to a significant reduction in the number of explicit water molecules required to model hydration effects.
Author: Slavica Jonic Publisher: Frontiers Media SA ISBN: 2889456994 Category : Languages : en Pages : 128
Book Description
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: Michael Feig Publisher: John Wiley & Sons ISBN: 3527629262 Category : Science Languages : en Pages : 334
Book Description
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: John Thomas Mongan Publisher: ISBN: Category : Languages : en Pages : 163
Book Description
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: Ariel Fernández Publisher: Springer ISBN: 3319308521 Category : Science Languages : en Pages : 490
Book Description
This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood without dealing with interfacial behaviour. There is an urge to grasp how biologically relevant behaviour is shaped by the structuring of biomolecular interfaces and how interfacial tension affects the molecular events that take place in the cell. This book squarely addresses these needs from a physicist perspective. The book may serve as a monograph for practitioners and, alternatively, as an advanced textbook. Fruitful reading requires a background in physical chemistry and some basics in biophysics. The selected problems at the end of the chapters and the progression in conceptual difficulty make it a suitable textbook for a graduate level course or an elective course for seniors majoring in chemistry, physics, biomedical engineering or related disciplines.
Author: Ilya D. Gridnev Publisher: CRC Press ISBN: 1498726550 Category : Science Languages : en Pages : 234
Book Description
The field of asymmetric catalysis is currently one of the hottest areas in chemistry. This unique book focuses on the mechanism of enantioselectivity in asymmetric catalysis, rather than asymmetric catalysis from the synthetic view. It describes reliable, experimentally and computationally supported mechanisms, and discusses the danger of so-called "plausible" or "accepted" mechanisms leading to wrong conclusions. It draws parallels to enzymatic catalysis in biochemistry, and examines in detail the physico-chemical aspects of enantioselective catalysis.
Author: Adam Liwo Publisher: Springer ISBN: 3319958437 Category : Technology & Engineering Languages : en Pages : 851
Book Description
This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.
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Author: Michael S. Lee
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Author: Slavica Jonic
Author: Michael Feig
Author: John Thomas Mongan
Author: Ariel Fernández
Author: [Anonymus AC06579881]
Author: Ilya D. Gridnev
Author: Adam Liwo