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Optimizing Potentials For Protein Structure Prediction Inverse Protein Folding And Protein Folding
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Book Synopsis Optimizing Potentials for Protein Structure Prediction, Inverse Protein Folding and Protein Folding by : Ting-Lan Chiu
Download or read book Optimizing Potentials for Protein Structure Prediction, Inverse Protein Folding and Protein Folding written by Ting-Lan Chiu and published by . This book was released on 1999 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Protein Folding Problem and Tertiary Structure Prediction by : Kenneth M.Jr. Merz
Download or read book The Protein Folding Problem and Tertiary Structure Prediction written by Kenneth M.Jr. Merz and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 585 pages. Available in PDF, EPUB and Kindle. Book excerpt: A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.
Book Synopsis Computational Methods for Protein Folding, Volume 120 by : Richard A. Friesner
Download or read book Computational Methods for Protein Folding, Volume 120 written by Richard A. Friesner and published by John Wiley & Sons. This book was released on 2004-04-07 with total page 544 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the first attempts to model proteins on a computer began almost thirty years ago, our understanding of protein structure and dynamics has dramatically increased. Spectroscopic measurement techniques continue to improve in resolution and sensitivity, allowing a wealth of information to be obtained with regard to the kinetics of protein folding and unfolding, and complementing the detailed structural picture of the folded state. Concurrently, algorithms, software, and computational hardware have progressed to the point where both structural and kinetic problems may be studied with a fair degree of realism. Despite these advances, many major challenges remain in understanding protein folding at both the conceptual and practical levels. Computational Methods for Protein Folding seeks to illuminate recent advances in computational modeling of protein folding in a way that will be useful to physicists, chemists, and chemical physicists. Covering a broad spectrum of computational methods and practices culled from a variety of research fields, the editors present a full range of models that, together, provide a thorough and current description of all aspects of protein folding. A valuable resource for both students and professionals in the field, the book will be of value both as a cutting-edge overview of existing information and as a catalyst for inspiring new studies. Computational Methods for Protein Folding is the 120th volume in the acclaimed series Advances in Chemical Physics, a compilation of scholarly works dedicated to the dissemination of contemporary advances in chemical physics, edited by Nobel Prize-winner Ilya Prigogine.
Book Synopsis Protein Structure Prediction by : Mohammed Zaki
Download or read book Protein Structure Prediction written by Mohammed Zaki and published by Springer Science & Business Media. This book was released on 2007-09-12 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers elements of both the data-driven comparative modeling approach to structure prediction and also recent attempts to simulate folding using explicit or simplified models. Despite the unsolved mystery of how a protein folds, advances are being made in predicting the interactions of proteins with other molecules. Also rapidly advancing are the methods for solving the inverse folding problem, the problem of finding a sequence to fit a structure. This book focuses on the various computational methods for prediction, their successes and their limitations, from the perspective of their most well known practitioners.
Book Synopsis Inverse Protein Folding, Hierarchical Optimisation and Tie Knots by : T. M. A. Fink
Download or read book Inverse Protein Folding, Hierarchical Optimisation and Tie Knots written by T. M. A. Fink and published by . This book was released on 1998 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Design of Proteins and a Protein Folding Potential by : Tanya Kurosky
Download or read book Design of Proteins and a Protein Folding Potential written by Tanya Kurosky and published by . This book was released on 1997 with total page 150 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Folds written by Henrik Bohr and published by CRC Press. This book was released on 1995-10-20 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by outstanding scientists in physics and molecular biology, this book addresses the most recent advances in the analysis of the protein folding processes and protein structure determination. Emphasis is also placed on modelling and presentation of experimental results of structural membrane bound proteins. Many color plates help to illustrate structural aspects covered including: Defining folds of protein domains Structure determination from sequence Distance geometry Lattice theories Membrane proteins Protein-Ligand interaction Topological considerations Docking onto receptors All analysis is presented with proven theory and experimentation. Protein Folds: A Distance-Based Approach is an excellent text/reference for biotechnologists and biochemists as well as graduate students studying in the research sciences.
Book Synopsis Optimized Protein Structure Prediction Through Hierarchical Dissections of Conformation Space by : Steven Z. Fairchild
Download or read book Optimized Protein Structure Prediction Through Hierarchical Dissections of Conformation Space written by Steven Z. Fairchild and published by . This book was released on 2007 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Folding and Self-Avoiding Walks Polyhedral Studies and Solutions by : Agnes Dittel
Download or read book Protein Folding and Self-Avoiding Walks Polyhedral Studies and Solutions written by Agnes Dittel and published by Logos Verlag Berlin GmbH. This book was released on 2008 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: The protein folding problem refers to the correlation of a protein's amino acid sequence and its native three-dimensional structure which is essential for functionality. It still constitutes one of the major challenges in computational biology. One commonly studied model for the protein folding problem is the HP lattice model in which proteins are considered in a fairly abstract representation. However, the HP model proteins exhibit significant parallels to proteins occurring in nature. The solution of the HP lattice mode as a combinatorial optimization problem has been proven to be NP-complete, and there have already been developed various different approaches for efficient algorithms. We study an integer programming formulation of the problem. Starting with an analysis of this model, where we concentrate on symmetry issues, we show how the model can be consolidated by exploiting symmetry properties of the underlying lattice. The main focus lies in the development of specific components of a branch-and-cut framework for the computation of solutions for the HP model by means of integer programming methods. In order to understand the structure of the model, we perform a series of polyhedral studies from which we derive two main classes of cutting planes. Furthermore, we exploit the knowledge of folding principles which are also valid for HP model proteins for the development of related branching strategies. For the solution of a special class of instances, we present an implementation of a genetic algorithm for the generation of primal feasible start solutions. Finally, we document the performance of the methods developed for each of the four topics (model consolidation, primal method, branching strategy and cutting planes) within the branch-and-cut procedure. We present computational results for different types of lattices, where we both consider known benchmark instances from literature and random instances.
Book Synopsis Protein Folding in Silico by : Irena Roterman-Konieczna
Download or read book Protein Folding in Silico written by Irena Roterman-Konieczna and published by Elsevier. This book was released on 2012-10-04 with total page 241 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. Discusses a range of ab initio models for protein structure prediction Introduces a unique model based on experimental observations Describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory
Book Synopsis Computational Protein Design by : Ilan Samish
Download or read book Computational Protein Design written by Ilan Samish and published by Humana. This book was released on 2016-12-03 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim this volume is to present the methods, challenges, software, and applications of this widespread and yet still evolving and maturing field. Computational Protein Design, the first book with this title, guides readers through computational protein design approaches, software and tailored solutions to specific case-study targets. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Protein Design aims to ensure successful results in the further study of this vital field.
Download or read book Protein Folding written by Charis Ghelis and published by Academic Press. This book was released on 2012-12-02 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Folding aims to collect the most important information in the field of protein folding and probes the main principles that govern formation of the three-dimensional structure of a protein from a nascent polypeptide chain, as well as how the functional properties appear. This text is organized into three sections and consists of 15 chapters. After an introductory chapter where the main problems of protein folding are considered at the cellular level in the context of protein biosynthesis, the discussion turns to the conformation of native globular proteins. Definitions and rules of nomenclature are given, including the structural organization of globular proteins deduced from X-ray crystallographic data. Folding mechanisms are tentatively deduced from the observation of invariants in the architecture of folded proteins. The next chapters focus on the energetics of protein conformation and structure, indicating the principles of thermodynamic stability of the native structure, along with theoretical computation studies of protein folding, structure prediction, and folding simulation. The reader is also introduced to various experimental approaches; the reversibility of the unfolding-folding process; equilibrium and kinetic studies; and detection and characterization of intermediates in protein folding. This text concludes with a chapter dealing with problems specific to oligomeric proteins. This book is intended for research scientists, specialists, biochemists, and students of biochemistry and biology.
Download or read book Protein Folding written by Alka Dwevedi and published by Springer. This book was released on 2014-12-01 with total page 61 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book will discuss classes of proteins and their folding, as well as the involvement of bioinformatics in solving the protein folding problem. In vivo and in vitro folding mechanisms are examined, as well as the failures of in vitro folding, a mechanism helpful in understanding disease caused by misfolding. The role of energy landscapes is also discussed and the computational approaches to these landscapes.
Book Synopsis Protein Structure Prediction by : Igor F. Tsigelny
Download or read book Protein Structure Prediction written by Igor F. Tsigelny and published by Internat'l University Line. This book was released on 2002 with total page 540 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Protein Stability and Folding by : Wolfgang Pfeil
Download or read book Protein Stability and Folding written by Wolfgang Pfeil and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 662 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding remains one of the most exclusive problems of modern biochemistry. Structure analysis has given access to the wealth of the molecular architecture of pro teins. As architecture needs static calculations, protein structure is always related to thermodynamic factors that govern folding and stability of a particular folded protein over the non-organized polypeptide chain. During the past decades a huge amount of thermodynamic data related to protein folding and stability has been accumulated. The data are certainly of importance in dechiffring the protein folding problem. At the same time, the data can guide the con struction of modified and newly synthesized proteins with properties optimized for particular application. The intention of this book is a generation of a data collection which makes the vast amount of present data accessible for multidisciplinary research where chemistry, phy sics, biology, and medicine are involved and also pharmaceutical and food research and technology. It took several years to compile all the data and the author wishes to thank everyone who provided data, ideas or even unpublished results. The author is, in particular, indebted to Prof. Wadso (Lund, Sweden) and IUPAC's Steering Committee on Bio physical Chemistry. Furthermore, support by the Deutsche Forschungsgemeinschafi (INK 16 AI-I) is acknowledged.
Book Synopsis Understanding the Determining Factors and Their Cooperative Effects on Protein Folding by : Yue Li
Download or read book Understanding the Determining Factors and Their Cooperative Effects on Protein Folding written by Yue Li and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: ABSTRACT: Protein is a linear chain of amino acids bonded by peptide bonds. Protein plays a vital role in almost every biological process. For most proteins, they need to fold into a stable 3D structure (native state) in order to function properly. This process that proteins fold from the sequence of amino acids to the 3D structure is known as protein folding. The relations among protein sequence, structure and function have been studied for many years in lab by expensive experimental methods such as X-ray crystallography and NMR spectroscopy. The emerging high performance microprocessors enable efficient and accurate protein structure simulation. Despite extensive studies previously, the factors behind the protein folding and their cooperative effects are still not completely understood. This dissertation presents the methods and results about investigating the determining factors for protein folding and their cooperative effects. We start with a simplified protein folding model, three-dimensional hydrophobic-polar (HP) model which only care about the hydrophobic interaction because it is believed that the hydrophobic interaction between residues is the driving force for protein folding. Although HP model is simple, it is useful enough to provide us a platform to measure the stability of protein which will eventually benefit us in the design of protein sequences. The funnel-shape energy landscape theory [2][3] states that a protein can fold into its specific three-dimensional structure through multiple pathways. There are many local minima during the process of folding. Protein can be trapped in these local minima temporarily, but eventually it will be guided towards the native state. Therefore, energy landscape entropy (ELE) is proposed to measure the foldability of a protein sequence. Based on our experimental results, the proportion of hydrophobic residues which is defined as hydrophobic content (HC) plays a determining role in the foldability of a protein sequence. A specific range of HC is the key for HP sequences to maintain the stability. To compare our simulation results with real protein sequences, we probed the proportion of hydrophobic residues values in a set of non-homologous globular proteins. We also reviewed the HC values of sequences of intrinsically disordered proteins (IDPs) from DisProt database. We then compared the hydrophobic contents between globular proteins and intrinsically disordered proteins (IDPs). We found that IDPs tend to occupy the lower range in the HC spectrum which matches the fact that IDPs have marginally stable states in their energy landscapes. The research on the proportion of hydrophobic residues shed a light on the protein design because it will prune the astronomical space of protein sequences. Previously, we have to enumerate every possible protein sequence in order to design a protein with specified function. With the aid of the knowledge about the proportion of hydrophobic residues, we can exclude a large number of redundant sequences whose proportion of hydrophobic residues is not eligible. However, the protein folding is a complicated process affected by multiple factors. In order to investigate these factors and their cooperative effects, an optimized energy function on a more realistic protein model is required. The quality of an energy function is the key of the success in protein structure prediction. Optimizing an energy function is a non-trivial problem in protein structure prediction. We propose to optimize the weights associated with energy terms by using the near native structures (NNS). The near native structure (NNS) is defined as the set of conformation whose side-chain dihedral angles are within a certain degree away from the native structure in this dissertation. The near native structure provides us an opportunity to assess the quality of an energy function. Correspondingly, the probability of the near native structure for a single type of residue is proposed. The optimized energy function will minimize the probability of the near native structure. The results indicate that our method invariably improve the average probability of the near native structure. We also find the similarity in the topology of side-chain infers the similar weights. However, there is no general configuration of weights for all twenty types of amino acids under current energy function. It is obvious that not all the determining factors are integrated into the current model consisting of only five energy terms. The current energy function is too coarse-grained to reflect the cooperative effects of all determining factors. When scientists design the energy function for protein structure prediction, it should be noted that the energy function should be fine-grained enough to disclose all the determining factors behind protein folding.
Book Synopsis A Metaheuristic Approach to Protein Structure Prediction by : Nanda Dulal Jana
Download or read book A Metaheuristic Approach to Protein Structure Prediction written by Nanda Dulal Jana and published by Springer. This book was released on 2018-03-05 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces characteristic features of the protein structure prediction (PSP) problem. It focuses on systematic selection and improvement of the most appropriate metaheuristic algorithm to solve the problem based on a fitness landscape analysis, rather than on the nature of the problem, which was the focus of methodologies in the past. Protein structure prediction is concerned with the question of how to determine the three-dimensional structure of a protein from its primary sequence. Recently a number of successful metaheuristic algorithms have been developed to determine the native structure, which plays an important role in medicine, drug design, and disease prediction. This interdisciplinary book consolidates the concepts most relevant to protein structure prediction (PSP) through global non-convex optimization. It is intended for graduate students from fields such as computer science, engineering, bioinformatics and as a reference for researchers and practitioners.
