Author: Marian Marko Nanias
Publisher:
ISBN:
Category :
Languages : en
Pages : 292

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Book Description

Author: Marian Nanias
Publisher:
ISBN: 9780542535789
Category :
Languages : en
Pages : 165

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Book Description
A hierarchical approach, together with the United Residue (UNRES) model of the polypeptide chain, is used to study protein structure prediction.

Author: Andrzej Koliński
Publisher: Landes Bioscience
ISBN:
Category : Medical
Languages : en
Pages : 224

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Book Description

Author: Leonidas Kapsokalyvas
Publisher:
ISBN:
Category : Lattice theory
Languages : en
Pages : 340

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Book Description
Abstract. Protein folding is the physical process in which a protein acquires its structure that allows it to perform a specific biological task. Proteins fold spon-taneously into three-dimensional structures of minimum energy when found in the appropriate environment. The study of this phenomenon is often facilitated through local search-based computer simulations in which the energy of a protein is mini¬mized. This thesis is concerned with local search methods for protein folding simulations in rectangular and triangular lattice models as well as in a simplified coarse-grained off-lattice model. The aim of those simulations is on the one hand protein struc¬ture prediction and on the other hand energy landscape analysis. Lattice models are often useful in the study of protein folding, since they allow exact enumeration of solutions, easy identification of local minima and paths leading to them. The challenge for local search-based methods in lattice model simulations is to efficiently sample an exponentially large search space. In that respect this thesis contributes a method to reduce the search space in rectangular lattices, which is adapted into specific neighborhood relations and is used in local search methods. This method is based on restricting search to a reduced subspace of protein structures, free from some special symmetrical versions of the same structure. The thesis also contributes a novel local search method for protein structure prediction, namely a population based local search. The novel local search method can be used to gather local min¬ima of the underlying energy landscape. The method outperforms the state-of-the-art method tested for the specific set of benchmarks in the cubic lattice and the MJ(Miyazawa-Jernigan) energy model. The survey of the energy landscape in the latter model reveals that the energy of local minima follows a Gaussian-like distri¬bution.

Author: Guangjie Shi
Publisher:
ISBN:
Category :
Languages : en
Pages : 200

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Book Description
Protein folding is studied within the context of two coarse-grained lattice models that separate all amino acids into only a few types. The hydrophobic-polar (HP) model is a simplified lattice protein model for simulating protein folding and for understanding many biological problems of interest. In this work, an "improved" model, the semi-flexible H0P model, was proposed by introducing a new type of "neutral" monomer, "0", i.e., neither hydrophobic nor polar and also taking into consideration the stiffness of bonds connecting monomers. Even though both models are highly simplified protein models, finding the lowest energy conformations and determining the density of states are extremely difficult. We applied replica-exchange Wang-Landau sampling with appropriate trial moves for determining the density of states of multiple HP and H0P proteins, from which the thermodynamic properties such as specific heat can be calculated. Moreover, we developed a heuristic method for determining the ground state degeneracy of lattice proteins, based on multicanonical sampling. It is applied during comprehensive studies of single-site mutations in specific lattice proteins with different sequences. The effects in which we are interested include structural changes in ground states, changes of ground state energy, degeneracy, and thermodynamic properties of the system. With respect to mutations, both extremely sensitive and insensitive positions in the protein sequence have been found. That is, ground state energies and degeneracies, as well as other thermodynamic and structural quantities may be either largely unaffected or may change significantly due to mutation. Moreover, comparison between the HP model and the semi-flexible H0P model have been performed based on two real proteins: Crambin and Ribonuclease A. We found that, compared with the HP model, the semi-flexible H0P model possesses significantly reduced ground state degeneracy, and rich folding signals as the proteins rearranging into native states from very compact structures at low temperatures. We calculated the free energy vs end-to-end distance as a function of temperature. The HP model shows a relatively shallow folding funnel and flat free energy minimum, reflecting the high degeneracy of the ground state. In contrast, the semi-flexible H0P model has a well developed, rough free energy funnel with a low degeneracy ground state. In both cases, folding funnels are asymmetric with temperature dependent shape.

Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 24

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Book Description
This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.

Author: Gregory A. Voth
Publisher: CRC Press
ISBN: 1420059564
Category : Science
Languages : en
Pages : 492

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Book Description
Exploring 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: Cláudio M. Gomes
Publisher: Springer
ISBN: 331900882X
Category : Science
Languages : en
Pages : 63

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Book Description
This snapshot volume is designed to provide a smooth entry into the field of protein folding. Presented in a concise manner, each section introduces key concepts while providing a brief overview of the relevant literature. Outlook subsections will pinpoint specific aspects related to emerging methodologies, concepts and trends.

Author: Garegin A. Papoian
Publisher: CRC Press
ISBN: 1315356708
Category : Science
Languages : en
Pages : 399

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Book Description
"The chapters in this book survey the progress in simulating biomolecular dynamics.... The images conjured up by this work are not yet universally loved, but are beginning to bring new insights into the study of biological structure and function. The future will decide whether this scientific movement can bring forth its Picasso or Modigliani." –from the Foreword by Peter G. Wolynes, Bullard-Welch Foundation Professor of Science, Rice University This book highlights the state-of-art in coarse-grained modeling of biomolecules, covering both fundamentals as well as various cutting edge applications. Coarse-graining of biomolecules is an area of rapid advances, with numerous new force fields having appeared recently and significant progress made in developing a systematic theory of coarse-graining. The contents start with first fundamental principles based on physics, then survey specific state-of-art coarse-grained force fields of proteins and nucleic acids, and provide examples of exciting biological problems that are at large scale, and hence, only amenable to coarse-grained modeling. Introduces coarse-grained models of proteins and nucleic acids. Showcases applications such as genome packaging in nuclei and understanding ribosome dynamics Gives the physical foundations of coarse-graining Demonstrates use of models for large-scale assemblies in modern studies Garegin A. Papoian is the first Monroe Martin Associate Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology at the University of Maryland.

Author: P. Michael Conn
Publisher: Academic Press
ISBN: 0080923399
Category : Science
Languages : en
Pages : 301

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Book Description
Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume. Follow the new editor-in-chief, P. Michael Conn, as he introduces this second thematic volume in the series – an in-depth aid to researchers who are looking for the best techniques and tools for understanding the complexities of protein folding Understand the advantages of protein folding over other therapeutic approaches and see how protein folding plays a critical role in the development of diseases such as Alzheimer’s and diabetes Decipher the rules of protein folding through compelling and timely reviews combined with chapters written by international authors in engineering, biochemistry, physics and computer science