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Biomolecular Assembly In Silico Using Massively Parallel Simulations To Probe Protein And Rna Folding Dynamics
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Book Synopsis Biomolecular Assembly in Silico Using Massively Parallel Simulations to Probe Protein and RNA Folding Dynamics by : Eric J. Sorin
Download or read book Biomolecular Assembly in Silico Using Massively Parallel Simulations to Probe Protein and RNA Folding Dynamics written by Eric J. Sorin and published by . This book was released on 2007 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Dynamic Simulation of Bio-molecular Dynamics, Folding, and Assembly by : Rongzhong Li
Download or read book Molecular Dynamic Simulation of Bio-molecular Dynamics, Folding, and Assembly written by Rongzhong Li and published by . This book was released on 2015 with total page 101 pages. Available in PDF, EPUB and Kindle. Book excerpt: It remains a major challenge in molecular biophysics to understand how biomolecules fold and interact with each other to carry out their cellular processes in a functional organism. Computational molecular dynamics (MD) simulations are indispensible tools for characterizing biomolecular processes at the microscopic level. In this thesis, I will present three distinct MD simulation studies of RNA folding, protein-RNA assembly, and protein-nanoparticle interaction mechanisms with direct comparisons to experiments whenever possible. I first present a coarse-grained and empirical force field MD simulations of tRNA. The coarse-grained MD simulations are based on the funneled energy landscape theory of biomolecular folding, and we perform tRNA folding TIS model MD simulations of four E. coli tRNAs with distinct sequences but very similar secondary and tertiary structures. The folding mechanisms are highly dependent on a sequence dependent base-stacking interaction term, demonstrating that the stabilities of the individual loops and stem determine the folding mechanism. We also matched melting profiles with classical empirically observed ones. The secondary structural elements can form in parallel if their stabilities are sufficiently similar, and this may explain why tRNAs have been shown experimentally to have fast and slow folding rates. We also observe the premature folding of some loops that must backtrack and completely unfold before folding to the native state can proceed. The backtracking mechanism has been predicted by simulations and verified in experiments in proteins, and our study is the first to predict the scenario for RNA molecules and it amenable to verification by experiments. Next, I present preliminary development of a novel protein-RNA complex assembly model for coarse-grained MD simulations. The model is applied to aminoacyltRNA synthetase in complex with its cognate tRNA molecule, specifically, a modeled MetRS:tRNA[superscript fMet] complex. The model is based on the native structure based Go-type model for proteins and the TIS model for RNA, but the introduction of the protein-RNA interactions is not trivial. Also, since these models were developed independently, matching their stabilities is a challenge. In our Go-TIS model Hamiltonian, we introduce protein-RNA interactions based on the Lorentz-Berthelot mixing rules and matched the empirical stabilities of the MetRS and tRNA[superscript fMet] separately. The model is not yet complete and we still have issues with regard to the binding stabilities. Finally, I present our novel GPU-optimizedMD simulation model of protein-nanoparticle interactions that was developed in collaboration with an experimental group. In this model, we use the Go-type model for proteins with an electrostatic term to describe the interactions between the charged residues and the charged citrate coated spherical nanoparticle. In excellent agreement with CD spectra, we observe the binding of the proteins to the nanoparticle surface, resulting in the melting of the secondary structure, notably the [alpha symbol]-helices. The percentage of helical melting is in quantitative agreement with our coarse-grained MD simulations.
Book Synopsis Molecular Modeling and Simulation by : Tamar Schlick
Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text
Book Synopsis Protein Simulations by : Valerie Daggett
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
Book Synopsis An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation by : Gregory R. Bowman
Download or read book An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation written by Gregory R. Bowman and published by Springer Science & Business Media. This book was released on 2013-12-02 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range of problems. The Markov state model (MSM) approach aims to address two key challenges of molecular simulation: 1) How to reach long timescales using short simulations of detailed molecular models. 2) How to systematically gain insight from the resulting sea of data. MSMs do this by providing a compact representation of the vast conformational space available to biomolecules by decomposing it into states sets of rapidly interconverting conformations and the rates of transitioning between states. This kinetic definition allows one to easily vary the temporal and spatial resolution of an MSM from high-resolution models capable of quantitative agreement with (or prediction of) experiment to low-resolution models that facilitate understanding. Additionally, MSMs facilitate the calculation of quantities that are difficult to obtain from more direct MD analyses, such as the ensemble of transition pathways. This book introduces the mathematical foundations of Markov models, how they can be used to analyze simulations and drive efficient simulations, and some of the insights these models have yielded in a variety of applications of molecular simulation.
Book Synopsis Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design by : Sanjeev Kumar Singh
Download or read book Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design written by Sanjeev Kumar Singh and published by Springer Nature. This book was released on 2021-02-02 with total page 334 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.
Book Synopsis Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs by : Sumit Sharma
Download or read book Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs written by Sumit Sharma and published by Elsevier. This book was released on 2019-08-09 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties. This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems
Book Synopsis Homology Molecular Modeling by : Rafael Trindade Maia
Download or read book Homology Molecular Modeling written by Rafael Trindade Maia and published by BoD – Books on Demand. This book was released on 2021-03-10 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Homology modeling is an extremely useful and versatile technique that is gaining more and more space and demand in research in computational and theoretical biology. This book, “Homology Molecular Modeling - Perspectives and Applications”, brings together unpublished chapters on this technique. In this book, 7 chapters are intimately related to the theme of molecular modeling, carefully selected and edited for academic and scientific readers. It is an indispensable read for anyone interested in the areas of bioinformatics and computational biology. Divided into 4 sections, the reader will have a didactic and comprehensive view of the theme, with updated and relevant concepts on the subject. This book was organized from researchers to researchers with the aim of spreading the fascinating area of molecular modeling by homology.
Book Synopsis Biomolecular Simulations by : Massimiliano Bonomi
Download or read book Biomolecular Simulations written by Massimiliano Bonomi and published by Humana. This book was released on 2020-08-14 with total page 581 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.
Book Synopsis Chemistry for the 21st Century by : Ehud Keinan
Download or read book Chemistry for the 21st Century written by Ehud Keinan and published by John Wiley & Sons. This book was released on 2001-02-08 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: Here, numerous winners of the Wolf prize from all chemical disciplines provide an overview of the new ideas and approaches that will shape this dynamic science over the forthcoming decades and so will have a decisive influence on our living conditions. This glimpse of the future is naturally based on the findings granted us by the rapid increase in chemical research during the 20th century. It may be said that a silent "revolution" took place, the positive results of which are still not fully predicted. For example, chemists in research laboratories nowadays are able to develop drugs in increasingly short times to treat diseases once thought incurable. They can design new materials that withstand extreme conditions, and predict the properties of compounds that no one has even seen yet. In this exceptional book those breakthroughs of modern chemistry are illustrated and explained by leading scientists. It stems from the high-quality papers given at the prestigious ceremony to accompany the presentation of the 20th Wolf Prize. It is an extraordinary source for every chemist in industry and academia to get an overview of the highlights of modern chemistry.
Book Synopsis Drug Discovery and Development by : Vishwanath Gaitonde
Download or read book Drug Discovery and Development written by Vishwanath Gaitonde and published by BoD – Books on Demand. This book was released on 2020-03-11 with total page 166 pages. Available in PDF, EPUB and Kindle. Book excerpt: The process of drug discovery and development is a complex multistage logistics project spanned over 10-15 years with an average budget exceeding 1 billion USD. Starting with target identification and synthesizing anywhere between 10k to 15k synthetic compounds to potentially obtain the final drug that reaches the market involves a complicated maze with multiple inter- and intra-operative fields. Topics described in this book emphasize the progresses in computational applications, pharmacokinetics advances, and molecular modeling developments. In addition the book also contains special topics describing target deorphaning in Mycobacterium tuberculosis, therapy treatment of some rare diseases, and developments in the pediatric drug discovery process.
Download or read book Modulation of Protein Function written by and published by . This book was released on 1979 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Epidemiology by : Paul A. Schulte
Download or read book Molecular Epidemiology written by Paul A. Schulte and published by Academic Press. This book was released on 2012-12-02 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book will serve as a primer for both laboratory and field scientists who are shaping the emerging field of molecular epidemiology. Molecular epidemiology utilizes the same paradigm as traditional epidemiology but uses biological markers to identify exposure, disease or susceptibility. Schulte and Perera present the epidemiologic methods pertinent to biological markers. The book is also designed to enumerate the considerations necessary for valid field research and provide a resource on the salient and subtle features of biological indicators.
Download or read book Virus Structure written by and published by Elsevier. This book was released on 2003-10-02 with total page 610 pages. Available in PDF, EPUB and Kindle. Book excerpt: Virus Structure covers the full spectrum of modern structural virology. Its goal is to describe the means for defining moderate to high resolution structures and the basic principles that have emerged from these studies. Among the topics covered are Hybrid Vigor, Structural Folds of Viral Proteins, Virus Particle Dynamics, Viral Gemone Organization, Enveloped Viruses and Large Viruses. Covers viral assembly using heterologous expression systems and cell extracts Discusses molecular mechanisms in bacteriophage T7 procapsid assembly, maturation and DNA containment Includes information on structural studies on antibody/virus complexes
Book Synopsis Membrane Organization and Dynamics by : Amitabha Chattopadhyay
Download or read book Membrane Organization and Dynamics written by Amitabha Chattopadhyay and published by Springer. This book was released on 2017-12-06 with total page 387 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume brings together information on membrane organization and dynamics from a variety of spectroscopic, microscopic and simulation approaches, spanning a broad range of time scales. The implication of such dynamic information on membrane function in health and disease is a topic of contemporary interest. The chapters cover various aspects of membrane lipid and protein dynamics, explored using a battery of experimental and theoretical approaches. The synthesis of information and knowledge gained by utilizing multiple approaches will provide the reader with a comprehensive understanding of the underlying membrane dynamics and function, which will help to develop robust dynamic models for the understanding of membrane function in healthy and diseased states. In the last few years, crystal structures of an impressive number of membrane proteins have been reported, thanks to tremendous advances in membrane protein crystallization techniques. Some of these recently solved structures belong to the G protein-coupled receptor (GPCR) family, which are particularly difficult to crystallize due to their intrinsic flexibility. Nonetheless, these static structures do not provide the necessary information to understand the function of membrane proteins in the complex membrane milieu. This volume will address the dynamic nature of membrane proteins within the membrane and will provide the reader with an up-to date overview of the theory and practical approaches that can be used. This volume will be invaluable to researchers working in a wide range of scientific areas, from biochemistry and molecular biology to biophysics and protein science. Students of these fields will also find this volume very useful. This book will also be of great use to those who are interested in the dynamic nature of biological processes.
Book Synopsis Mathematical Modelling in Biomedicine by : Vitaly Volpert
Download or read book Mathematical Modelling in Biomedicine written by Vitaly Volpert and published by MDPI. This book was released on 2021-01-26 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical modelling in biomedicine is a rapidly developing scientific discipline at the intersection of medicine, biology, mathematics, physics, and computer science. Its progress is stimulated by fundamental scientific questions and by the applications to public health. This book represents a collection of papers devoted to mathematical modelling of various physiological problems in normal and pathological conditions. It covers a broad range of topics including cardiovascular system and diseases, heart and brain modelling, tumor growth, viral infections, and immune response. Computational models of blood circulation are used to study the influence of heart arrhythmias on coronary blood flow and on operating modes for left-ventricle-assisted devices. Wave propagation in the cardiac tissue is investigated in order to show the influence of tissue heterogeneity and fibrosis. The models of tumor growth are used to determine optimal protocols of antiangiogenic and radiotherapy. The models of viral hepatitis kinetics are considered for the parameter identification, and the evolution of viral quasi-species is investigated. The book presents the state-of-the-art in mathematical modelling in biomedicine and opens new perspectives in this passionate field of research.
Book Synopsis Computational Modeling And Simulations Of Biomolecular Systems by : Benoit Roux
Download or read book Computational Modeling And Simulations Of Biomolecular Systems written by Benoit Roux and published by World Scientific. This book was released on 2021-08-23 with total page 209 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).
