Protein Tertiary Structure Prediction Via Global Optimization Of Reduced Model Potential Energy Functions

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Computational Methods for Protein Folding, Volume 120

Author : Richard A. Friesner
Publisher : John Wiley & Sons
ISBN 13 : 0471465232
Total Pages : 544 pages
Book Rating : 4.4/5 (714 download)

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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.

Optimization in Computational Chemistry and Molecular Biology

Author : Christodoulos A. Floudas
Publisher : Springer Science & Business Media
ISBN 13 : 147573218X
Total Pages : 341 pages
Book Rating : 4.4/5 (757 download)

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Book Synopsis Optimization in Computational Chemistry and Molecular Biology by : Christodoulos A. Floudas

Download or read book Optimization in Computational Chemistry and Molecular Biology written by Christodoulos A. Floudas and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches covers recent developments in optimization techniques for addressing several computational chemistry and biology problems. A tantalizing problem that cuts across the fields of computational chemistry, biology, medicine, engineering and applied mathematics is how proteins fold. Global and local optimization provide a systematic framework of conformational searches for the prediction of three-dimensional protein structures that represent the global minimum free energy, as well as low-energy biomolecular conformations. Each contribution in the book is essentially expository in nature, but of scholarly treatment. The topics covered include advances in local and global optimization approaches for molecular dynamics and modeling, distance geometry, protein folding, molecular structure refinement, protein and drug design, and molecular and peptide docking. Audience: The book is addressed not only to researchers in mathematical programming, but to all scientists in various disciplines who use optimization methods in solving problems in computational chemistry and biology.

Dissertation Abstracts International

Author :
Publisher :
ISBN 13 :
Total Pages : 846 pages
Book Rating : 4.F/5 ( download)

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Book Synopsis Dissertation Abstracts International by :

Download or read book Dissertation Abstracts International written by and published by . This book was released on 2000 with total page 846 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Methods for Protein Structure Prediction and Modeling

Author : Ying Xu
Publisher : Springer Science & Business Media
ISBN 13 : 0387683720
Total Pages : 408 pages
Book Rating : 4.3/5 (876 download)

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Book Synopsis Computational Methods for Protein Structure Prediction and Modeling by : Ying Xu

Download or read book Computational Methods for Protein Structure Prediction and Modeling written by Ying Xu and published by Springer Science & Business Media. This book was released on 2007-08-24 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.

Comprehensive Biophysics

Author :
Publisher : Academic Press
ISBN 13 : 0080957188
Total Pages : 3533 pages
Book Rating : 4.0/5 (89 download)

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Book Synopsis Comprehensive Biophysics by :

Download or read book Comprehensive Biophysics written by and published by Academic Press. This book was released on 2012-04-12 with total page 3533 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysics is a rapidly-evolving interdisciplinary science that applies theories and methods of the physical sciences to questions of biology. Biophysics encompasses many disciplines, including physics, chemistry, mathematics, biology, biochemistry, medicine, pharmacology, physiology, and neuroscience, and it is essential that scientists working in these varied fields are able to understand each other's research. Comprehensive Biophysics, Nine Volume Set will help bridge that communication gap. Written by a team of researchers at the forefront of their respective fields, under the guidance of Chief Editor Edward Egelman, Comprehensive Biophysics, Nine Volume Set provides definitive introductions to a broad array of topics, uniting different areas of biophysics research - from the physical techniques for studying macromolecular structure to protein folding, muscle and molecular motors, cell biophysics, bioenergetics and more. The result is this comprehensive scientific resource - a valuable tool both for helping researchers come to grips quickly with material from related biophysics fields outside their areas of expertise, and for reinforcing their existing knowledge. Biophysical research today encompasses many areas of biology. These studies do not necessarily share a unique identifying factor. This work unites the different areas of research and allows users, regardless of their background, to navigate through the most essential concepts with ease, saving them time and vastly improving their understanding The field of biophysics counts several journals that are directly and indirectly concerned with the field. There is no reference work that encompasses the entire field and unites the different areas of research through deep foundational reviews. Comprehensive Biophysics fills this vacuum, being a definitive work on biophysics. It will help users apply context to the diverse journal literature offering, and aid them in identifying areas for further research Chief Editor Edward Egelman (E-I-C, Biophysical Journal) has assembled an impressive, world-class team of Volume Editors and Contributing Authors. Each chapter has been painstakingly reviewed and checked for consistent high quality. The result is an authoritative overview which ties the literature together and provides the user with a reliable background information and citation resource

Data Mining in Biomedicine

Author : Panos M. Pardalos
Publisher : Springer Science & Business Media
ISBN 13 : 038769319X
Total Pages : 577 pages
Book Rating : 4.3/5 (876 download)

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Book Synopsis Data Mining in Biomedicine by : Panos M. Pardalos

Download or read book Data Mining in Biomedicine written by Panos M. Pardalos and published by Springer Science & Business Media. This book was released on 2008-12-10 with total page 577 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents an extensive collection of contributions covering aspects of the exciting and important research field of data mining techniques in biomedicine. Coverage includes new approaches for the analysis of biomedical data; applications of data mining techniques to real-life problems in medical practice; comprehensive reviews of recent trends in the field. The book addresses incorporation of data mining in fundamental areas of biomedical research: genomics, proteomics, protein characterization, and neuroscience.

Chemical Abstracts

Author :
Publisher :
ISBN 13 :
Total Pages : 2710 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Chemical Abstracts by :

Download or read book Chemical Abstracts written by and published by . This book was released on 2002 with total page 2710 pages. Available in PDF, EPUB and Kindle. Book excerpt:

The Protein Folding Problem and Tertiary Structure Prediction

Author : Kenneth M.Jr. Merz
Publisher : Springer Science & Business Media
ISBN 13 : 1468468316
Total Pages : 585 pages
Book Rating : 4.4/5 (684 download)

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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.

Protein Structure Prediction

Author : Mohammed Zaki
Publisher : Springer Science & Business Media
ISBN 13 : 1588297527
Total Pages : 338 pages
Book Rating : 4.5/5 (882 download)

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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.

Advances in Evolutionary Computing

Author : Ashish Ghosh
Publisher : Springer Science & Business Media
ISBN 13 : 3642189652
Total Pages : 1001 pages
Book Rating : 4.6/5 (421 download)

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Book Synopsis Advances in Evolutionary Computing by : Ashish Ghosh

Download or read book Advances in Evolutionary Computing written by Ashish Ghosh and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 1001 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a collection of fourty articles containing new material on both theoretical aspects of Evolutionary Computing (EC), and demonstrating the usefulness/success of it for various kinds of large-scale real world problems. Around 23 articles deal with various theoretical aspects of EC and 17 articles demonstrate the success of EC methodologies. These articles are written by leading experts of the field from different countries all over the world.

Large-Scale Optimization with Applications

Author : Lorenz T. Biegler
Publisher : Springer Science & Business Media
ISBN 13 : 1461206936
Total Pages : 212 pages
Book Rating : 4.4/5 (612 download)

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Book Synopsis Large-Scale Optimization with Applications by : Lorenz T. Biegler

Download or read book Large-Scale Optimization with Applications written by Lorenz T. Biegler and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 212 pages. Available in PDF, EPUB and Kindle. Book excerpt: With contributions by specialists in optimization and practitioners in the fields of aerospace engineering, chemical engineering, and fluid and solid mechanics, the major themes include an assessment of the state of the art in optimization algorithms as well as challenging applications in design and control, in the areas of process engineering and systems with partial differential equation models.

Molecular Bioinformatics

Author : Steffen Schulze-Kremer
Publisher : Walter de Gruyter
ISBN 13 : 9783110141139
Total Pages : 324 pages
Book Rating : 4.1/5 (411 download)

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Book Synopsis Molecular Bioinformatics by : Steffen Schulze-Kremer

Download or read book Molecular Bioinformatics written by Steffen Schulze-Kremer and published by Walter de Gruyter. This book was released on 1996 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt:

From Protein Structure to Function with Bioinformatics

Author : Daniel J. Rigden
Publisher : Springer
ISBN 13 : 9402410694
Total Pages : 509 pages
Book Rating : 4.4/5 (24 download)

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Book Synopsis From Protein Structure to Function with Bioinformatics by : Daniel J. Rigden

Download or read book From Protein Structure to Function with Bioinformatics written by Daniel J. Rigden and published by Springer. This book was released on 2017-04-06 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is about protein structural bioinformatics and how it can help understand and predict protein function. It covers structure-based methods that can assign and explain protein function based on overall folds, characteristics of protein surfaces, occurrence of small 3D motifs, protein-protein interactions and on dynamic properties. Such methods help extract maximum value from new experimental structures, but can often be applied to protein models. The book also, therefore, provides comprehensive coverage of methods for predicting or inferring protein structure, covering all structural classes from globular proteins and their membrane-resident counterparts to amyloid structures and intrinsically disordered proteins. The book is split into two broad sections, the first covering methods to generate or infer protein structure, the second dealing with structure-based function annotation. Each chapter is written by world experts in the field. The first section covers methods ranging from traditional homology modelling and fold recognition to fragment-based ab initio methods, and includes a chapter, new for the second edition, on structure prediction using evolutionary covariance. Membrane proteins and intrinsically disordered proteins are each assigned chapters, while two new chapters deal with amyloid structures and means to predict modes of protein-protein interaction. The second section includes chapters covering functional diversity within protein folds and means to assign function based on surface properties and recurring motifs. Further chapters cover the key roles of protein dynamics in protein function and use of automated servers for function inference. The book concludes with two chapters covering case studies of structure prediction, based respectively on crystal structures and protein models, providing numerous examples of real-world usage of the methods mentioned previously. This book is targeted at postgraduate students and academic researchers. It is most obviously of interest to protein bioinformaticians and structural biologists, but should also serve as a guide to biologists more broadly by highlighting the insights that structural bioinformatics can provide into proteins of their interest.

Constrained Optimization and Lagrange Multiplier Methods

Author : Dimitri P. Bertsekas
Publisher : Academic Press
ISBN 13 : 148326047X
Total Pages : 412 pages
Book Rating : 4.4/5 (832 download)

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Book Synopsis Constrained Optimization and Lagrange Multiplier Methods by : Dimitri P. Bertsekas

Download or read book Constrained Optimization and Lagrange Multiplier Methods written by Dimitri P. Bertsekas and published by Academic Press. This book was released on 2014-05-10 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computer Science and Applied Mathematics: Constrained Optimization and Lagrange Multiplier Methods focuses on the advancements in the applications of the Lagrange multiplier methods for constrained minimization. The publication first offers information on the method of multipliers for equality constrained problems and the method of multipliers for inequality constrained and nondifferentiable optimization problems. Discussions focus on approximation procedures for nondifferentiable and ill-conditioned optimization problems; asymptotically exact minimization in the methods of multipliers; duality framework for the method of multipliers; and the quadratic penalty function method. The text then examines exact penalty methods, including nondifferentiable exact penalty functions; linearization algorithms based on nondifferentiable exact penalty functions; differentiable exact penalty functions; and local and global convergence of Lagrangian methods. The book ponders on the nonquadratic penalty functions of convex programming. Topics include large scale separable integer programming problems and the exponential method of multipliers; classes of penalty functions and corresponding methods of multipliers; and convergence analysis of multiplier methods. The text is a valuable reference for mathematicians and researchers interested in the Lagrange multiplier methods.

Advances in Convex Analysis and Global Optimization

Author : Nicolas Hadjisavvas
Publisher : Springer Science & Business Media
ISBN 13 : 146130279X
Total Pages : 601 pages
Book Rating : 4.4/5 (613 download)

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Book Synopsis Advances in Convex Analysis and Global Optimization by : Nicolas Hadjisavvas

Download or read book Advances in Convex Analysis and Global Optimization written by Nicolas Hadjisavvas and published by Springer Science & Business Media. This book was released on 2013-12-01 with total page 601 pages. Available in PDF, EPUB and Kindle. Book excerpt: There has been much recent progress in global optimization algo rithms for nonconvex continuous and discrete problems from both a theoretical and a practical perspective. Convex analysis plays a fun damental role in the analysis and development of global optimization algorithms. This is due essentially to the fact that virtually all noncon vex optimization problems can be described using differences of convex functions and differences of convex sets. A conference on Convex Analysis and Global Optimization was held during June 5 -9, 2000 at Pythagorion, Samos, Greece. The conference was honoring the memory of C. Caratheodory (1873-1950) and was en dorsed by the Mathematical Programming Society (MPS) and by the Society for Industrial and Applied Mathematics (SIAM) Activity Group in Optimization. The conference was sponsored by the European Union (through the EPEAEK program), the Department of Mathematics of the Aegean University and the Center for Applied Optimization of the University of Florida, by the General Secretariat of Research and Tech nology of Greece, by the Ministry of Education of Greece, and several local Greek government agencies and companies. This volume contains a selective collection of refereed papers based on invited and contribut ing talks presented at this conference. The two themes of convexity and global optimization pervade this book. The conference provided a forum for researchers working on different aspects of convexity and global opti mization to present their recent discoveries, and to interact with people working on complementary aspects of mathematical programming.

Computational Molecular Dynamics: Challenges, Methods, Ideas

Author : Peter Deuflhard
Publisher : Springer Science & Business Media
ISBN 13 : 3642583601
Total Pages : 500 pages
Book Rating : 4.6/5 (425 download)

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Book Synopsis Computational Molecular Dynamics: Challenges, Methods, Ideas by : Peter Deuflhard

Download or read book Computational Molecular Dynamics: Challenges, Methods, Ideas written by Peter Deuflhard and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.

Biomat 2005 - Proceedings Of The International Symposium On Mathematical And Computational Biology

Author : Rubem P Mondaini
Publisher : World Scientific
ISBN 13 : 9814478091
Total Pages : 409 pages
Book Rating : 4.8/5 (144 download)

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Book Synopsis Biomat 2005 - Proceedings Of The International Symposium On Mathematical And Computational Biology by : Rubem P Mondaini

Download or read book Biomat 2005 - Proceedings Of The International Symposium On Mathematical And Computational Biology written by Rubem P Mondaini and published by World Scientific. This book was released on 2006-04-25 with total page 409 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains the contributions of the keynote speakers to the BIOMAT 2005 symposium, as well as a collection of selected papers by pioneering researchers. It provides a comprehensive review of the mathematical modeling of cancer development, Alzheimer's disease, malaria, and aneurysm development. Various models for the immune system and epidemiological issues are analyzed and reviewed. The book also explores protein structure prediction by optimization and combinatorial techniques (Steiner trees). The coverage includes bioinformatics issues, regulation of gene expression, evolution, development, DNA and array modeling, and small world networks.