Download or read book Modeling the Interaction and Energetics of Biological Molecules with a Polarizable Force Field written by Yue Shi and published by . This book was released on 2013 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Accurate prediction of protein-ligand binding affinity is essential to computational drug discovery. Current approaches are limited by the accuracy of the underlying potential energy model that describes atomic interactions. A more rigorous physical model is critical for evaluating molecular interactions to chemical accuracy. The objective of this thesis research is to develop a polarizable force field with an accurate representation of electrostatic interactions, and apply this model to protein-ligand recognition and to ultimately solve practical problems in computer aided drug discovery. By calculating the hydration free energies of a series of organic small molecules, an optimal protocol is established to develop the electrostatic parameters from quantum mechanics calculations. Next, the systematical development and parameterization procedure of AMOEBA protein force field is presented. The derived force field has gone through extensive validations in both gas phase and condensed phase. The last part of the thesis involves the application of AMOEBA to study protein-ligand interactions. The binding free energies of benzamidine analogs to trypsin using molecular dynamics alchemical perturbation are calculated with encouraging accuracy. AMOEBA is also used to study the thermodynamic effect of constraining and hydrophobicity on binding energetics between phosphotyrosine(pY)-containing tripeptides and the SH2 domain of growth receptor binding protein 2 (Grb2). The underlying mechanism of an "entropic paradox" associated with ligand preorganization is explored.
Download or read book Many Body Effects and Electrostatics in Biomolecules written by Qiang Cui and published by CRC Press. This book was released on 2016-03-30 with total page 590 pages. Available in PDF, EPUB and Kindle. Book excerpt: As computational hardware continues to develop at a rapid pace, quantitative computations are playing an increasingly essential role in the study of biomolecular systems. One of the most important challenges that the field faces is to develop the next generation of computational models that strike the proper balance of computational efficiency and
Download or read book Modeling Solvent Environments written by Michael Feig and published by John Wiley & Sons. This book was released on 2009-12-09 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Chemical Theory and Multiscale Simulation in Biomolecules written by Guohui Li and published by Elsevier. This book was released on 2024-03-29 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecules can provide, and how to compare this information with experiments. Beginning with an introduction to computational theory for modeling, the book goes on to describe how to control the conditions of modeling systems and possible strategies for time-cost savings in computation. Part Two further outlines key methods, with step-by-step guidance supporting readers in studying and practicing simulation processes. Part Three then shows how these theories are controlled and applied in practice, through examples and case studies on varied applications. This book is a practical guide for new learners, supporting them in learning and applying molecular modeling in practice, whilst also providing more experienced readers with the knowledge needed to gain a deep understanding of the theoretical background behind key methods. - Presents computational theory alongside case studies to help readers understand the use of simulation in practice - Includes extensive examples of different types of simulation methods and approaches to result analysis - Provides an overview of the current academic frontier and research challenges, encouraging creativity and directing attention to current problems
Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts.
Download or read book Developing the Polarizable Force Field Focus on Amino Acid Residues written by Qina Sa and published by . This book was released on 2011 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Polarizable force field has been successfully used in molecular modeling for years, especially in biological and protein simulations. In this research thesis, development of a new polarizable force field ―POSSIM (POlarizable Simulations with Second order Interaction Model) involving electrostatic polarization is described and parameters for several protein residues were produced. In this research thesis, the POSSIM force field was extended to the side chains of the following residues: lysine, glutamic acid, prontonated hisidine, phenylalanine and tryptophan. This work involved producing parameters for methyl ammonium, acetate ion, imidazolium cation, benzene and pyrrole molecules. The parameters fitting procedure starts from the molecular complex with dipolar electrostatic probes of a many-body system to produce polarizabilities, compute the energies, then charges and Lennard-Jones parameters are produced by fitting to gas-phase dimerization calculations, followed by the torsional parameters fitting and end up with the pure liquid simulations. In all the cases, three-body energies, dimerization energies and distances agree well to the accurate quantum mechanical results. The final parameters obtained assured the error of less than 2% in the heat of vaporization and average volume results compared with the available experimental data. Unlike the quantum mechanical calculations, the polarizable force field computations require a relatively small amount of computational resources. Moreover, compared to fixed-charges empirical force fields, polarizable force fields are much more accurate in a number of energy calculations. In the following chapters, the results obtained with this particular polarizable force field are discussed.
Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012-05-24 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Molecular Modeling at the Atomic Scale written by Ruhong Zhou and published by CRC Press. This book was released on 2014-08-21 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although molecular modeling has been around for a while, the groundbreaking advancement of massively parallel supercomputers and novel algorithms for parallelization is shaping this field into an exciting new area. Developments in molecular modeling from experimental and computational techniques have enabled a wide range of biological applications. Responding to this renaissance, Molecular Modeling at the Atomic Scale: Methods and Applications in Quantitative Biology includes discussions of advanced techniques of molecular modeling and the latest research advancements in biomolecular applications from leading experts. The book begins with a brief introduction of major methods and applications, then covers the development of cutting-edge methods/algorithms, new polarizable force fields, and massively parallel computing techniques, followed by descriptions of how these novel techniques can be applied in various research areas in molecular biology. It also examines the self-assembly of biomacromolecules, including protein folding, RNA folding, amyloid peptide aggregation, and membrane lipid bilayer formation. Additional topics highlight biomolecular interactions, including protein interactions with DNA/RNA, membrane, ligands, and nanoparticles. Discussion of emerging topics in biomolecular modeling such as DNA sequencing with solid-state nanopores and biological water under nanoconfinement round out the coverage. This timely summary contains the perspectives of leading experts on this transformation in molecular biology and includes state-of-the-art examples of how molecular modeling approaches are being applied to critical questions in modern quantitative biology. It pulls together the latest research and applications of molecular modeling and real-world expertise that can boost your research and development of applications in this rapidly changing field.
Download or read book Quantum Chemistry Simulation of Biological Molecules written by Eudenilson L. Albuquerque and published by Cambridge University Press. This book was released on 2021-02-11 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers quantum chemical simulation of molecular systems and their quantum chemical properties, alongside the most cutting-edge biomedical applications.
Download or read book Solvation Effects on Molecules and Biomolecules written by Sylvio Canuto and published by Springer Science & Business Media. This book was released on 2010-07-03 with total page 536 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is an interdisciplinary treatise on the theoretical approach to solvation problems. It describes the essential details of the theoretical methods and places them into the context of modern applications, and hence is of broad interest to theoreticians and experimentalists. The assembly of these modern methods and applications into one volume is a unique contribution to date and gives a broad and ample description of the field in its present stage of development.
Download or read book Molecular Materials with Specific Interactions Modeling and Design written by W. Andrzej Sokalski and published by Springer Science & Business Media. This book was released on 2007-05-06 with total page 597 pages. Available in PDF, EPUB and Kindle. Book excerpt: Design of new molecular materials is emerging as a new interdisciplinary research field. Corresponding reports are scattered in literature, and this book constitutes one of the first attempts to overview ongoing research efforts. It provides basic information, as well as the details of theory and examples of its application, to experimentalists and theoreticians interested in modeling molecular properties and putting into practice rational design of new materials.
Download or read book Protein Simulations written by Valerie Daggett and published by Elsevier. This book was released on 2003-11-26 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein 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
Download or read book Ion Modeling and Ligand protein Binding Calculation with a Polarizable Force Field written by Dian Jiao and published by . This book was released on 2009 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: Specific recognition of ligands including metal ions by proteins is the key of many crucial biological functions and systems. Accurate prediction of the binding strength not only sheds light on the mechanism of the molecular recognition but also provides the most important prerequisite of drug discovery. Computational modeling of molecular binding has gained a great deal of attentions in the last few decades since the advancement of computer power and availability of high-resolution crystal structures. However there still exist two major challenges in the field of molecular modeling, i.e. sampling issue and accuracy of the models. In this work, I have dedicated to tackling these two problems with a noval polarizable force field which is believed to produce more accurate description of molecular interactions than classic non-polarizable force fields. We first developed the model for divalent cations Mg2 and Ca2, deriving the parameters from quantum mechanics. To understand the hydration thermodynamics of these ions we have performed molecular dynamics simulations using our AMOEBA force field. Both the water structures around ions and the solvation free energies were in great accordance with experiment data. We have also simulated and calculated the binding free energies of a series of benzamidine-like inhibitors to trypsin using explicit solvent approach by free energy perturbation. The calculated binding free energies are well within the accuracy of experimental measurement and the direction of change is predicted correctly in all cases. Finally, we computed the hydration free energies of a few organic molecules and automated the calculation procedure.
Download or read book Protein Ligand Interactions written by Holger Gohlke and published by John Wiley & Sons. This book was released on 2012-04-06 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.
Download or read book Multi scale Quantum Models for Biocatalysis written by Darrin M. York and published by Springer Science & Business Media. This book was released on 2009-05-30 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: “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.
Download or read book A Physics based Intermolecular Potential for Biomolecular Simulation written by Joshua A. Rackers and published by . This book was released on 2019 with total page 289 pages. Available in PDF, EPUB and Kindle. Book excerpt: The grand challenge of biophysics is to use the fundamental laws of physics to predict how biological molecules will move and interact. The atomistic HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field is meant to address this challenge. It does so by breaking down the intermolecular potential energy function of biomolecular interactions into physically meaningful components (electrostatics, polarization, dispersion, and exchange-repulsion) and using this function to drive molecular dynamics simulations. This force field is able to achieve accuracy within 1 kcal/mol for each component when compared with ab initio Symmetry Adapted Perturbation Theory calculations. HIPPO is capable of this accuracy because it introduces a model electron density on every atom in the molecular system. Since the model is built on first-principles physics, it is transferable from small model systems to bulk phase. In the first test case, the HIPPO force field for water was able to reproduce the experimental density, heat of vaporization and dielectric constant to within 1%. Importantly, HIPPO has been shown to be only 10% more computationally expensive than the widely-used AMOEBA force field, meaning that more accurate simulations of larger biological molecules are well within reach.
Download or read book Computational Pharmaceutics written by Defang Ouyang and published by John Wiley & Sons. This book was released on 2015-07-20 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular modeling techniques have been widely used in drug discovery fields for rational drug design and compound screening. Now these techniques are used to model or mimic the behavior of molecules, and help us study formulation at the molecular level. Computational pharmaceutics enables us to understand the mechanism of drug delivery, and to develop new drug delivery systems. The book discusses the modeling of different drug delivery systems, including cyclodextrins, solid dispersions, polymorphism prediction, dendrimer-based delivery systems, surfactant-based micelle, polymeric drug delivery systems, liposome, protein/peptide formulations, non-viral gene delivery systems, drug-protein binding, silica nanoparticles, carbon nanotube-based drug delivery systems, diamond nanoparticles and layered double hydroxides (LDHs) drug delivery systems. Although there are a number of existing books about rational drug design with molecular modeling techniques, these techniques still look mysterious and daunting for pharmaceutical scientists. This book fills the gap between pharmaceutics and molecular modeling, and presents a systematic and overall introduction to computational pharmaceutics. It covers all introductory, advanced and specialist levels. It provides a totally different perspective to pharmaceutical scientists, and will greatly facilitate the development of pharmaceutics. It also helps computational chemists to look for the important questions in the drug delivery field. This book is included in the Advances in Pharmaceutical Technology book series.
