An Implicit Solvent Model for Biomolecular Monte Carlo Simulations
Author: Martin Brieg
Publisher:
Published: 2014
Total Pages:
ISBN-13:
DOWNLOAD EBOOKRead and Download eBook Full
Author: Martin Brieg
Publisher:
Published: 2014
Total Pages:
ISBN-13:
DOWNLOAD EBOOKAuthor: BenoƮt Roux
Publisher:
Published: 1999
Total Pages: 217
ISBN-13:
DOWNLOAD EBOOKAuthor: Roger Gregory
Publisher: CRC Press
Published: 1995-01-04
Total Pages: 596
ISBN-13: 9780824792398
DOWNLOAD EBOOKThis work covers advances in the interactions of proteins with their solvent environment and provides fundamental physical information useful for the application of proteins in biotechnology and industrial processes. It discusses in detail structure, dynamic and thermodynamic aspects of protein hydration, as well as proteins in aqueous and organic solvents as they relate to protein function, stability and folding.
Author: Tamar Schlick
Publisher: Royal Society of Chemistry
Published: 2012-05-24
Total Pages: 381
ISBN-13: 1849735042
DOWNLOAD EBOOKThe 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:
Publisher:
Published: 2004
Total Pages: 18
ISBN-13:
DOWNLOAD EBOOKIn 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: Valerie Daggett
Publisher: Elsevier
Published: 2003-11-26
Total Pages: 477
ISBN-13: 0080493785
DOWNLOAD EBOOKProtein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
Author: Michael S. Lee
Publisher:
Published: 2004
Total Pages: 18
ISBN-13:
DOWNLOAD EBOOKIn 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 Feig
Publisher: John Wiley & Sons
Published: 2009-12-09
Total Pages: 334
ISBN-13: 3527629262
DOWNLOAD EBOOKA 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: Gregory A. Voth
Publisher: CRC Press
Published: 2008-09-22
Total Pages: 492
ISBN-13: 1420059564
DOWNLOAD EBOOKExploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.
Author: Ling Zhang
Publisher:
Published: 2006
Total Pages: 380
ISBN-13:
DOWNLOAD EBOOK