Computational Optimization Algorithms For Protein Structure Refinement

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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.

Current Methods and Optimization Algorithms for the Refinement of X-Ray Crystal Structures

Author : J. Uria
Publisher : CRC Press
ISBN 13 : 9789056992514
Total Pages : 78 pages
Book Rating : 4.9/5 (925 download)

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Book Synopsis Current Methods and Optimization Algorithms for the Refinement of X-Ray Crystal Structures by : J. Uria

Download or read book Current Methods and Optimization Algorithms for the Refinement of X-Ray Crystal Structures written by J. Uria and published by CRC Press. This book was released on 1999-08-19 with total page 78 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Optimization in Computational Chemistry and Molecular Biology

Author : Christodoulos A. Floudas
Publisher : Springer Science & Business Media
ISBN 13 : 9780792361558
Total Pages : 362 pages
Book Rating : 4.3/5 (615 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 2000-02-29 with total page 362 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.

Computational Modeling and Simulation in Biomedical Research

Author : Yee Siew Choong
Publisher : Bentham Science Publishers
ISBN 13 : 981516547X
Total Pages : 159 pages
Book Rating : 4.8/5 (151 download)

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Book Synopsis Computational Modeling and Simulation in Biomedical Research by : Yee Siew Choong

Download or read book Computational Modeling and Simulation in Biomedical Research written by Yee Siew Choong and published by Bentham Science Publishers. This book was released on 2024-08-01 with total page 159 pages. Available in PDF, EPUB and Kindle. Book excerpt: This reference provides a comprehensive overview of computational modelling and simulation for theoretical and practical biomedical research. The book explains basic concepts of computational biology and data modelling for learners and early career researchers. Chapters cover these topics: 1. An introduction to computational tools in biomedical research 2. Computational analysis of biological data 3. Algorithm development for computational modelling and simulation 4. The roles and application of protein modelling in biomedical research 5. Dynamics of biomolecular ligand recognition Key features include a simple, easy-to-understand presentation, detailed explanation of important concepts in computational modeling and simulations and references.

Computational Structural Biology

Author : Torsten Schwede
Publisher : World Scientific
ISBN 13 : 9812778780
Total Pages : 790 pages
Book Rating : 4.8/5 (127 download)

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Book Synopsis Computational Structural Biology by : Torsten Schwede

Download or read book Computational Structural Biology written by Torsten Schwede and published by World Scientific. This book was released on 2008 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a comprehensive introduction to Landau-Lifshitz equations and Landau-Lifshitz-Maxwell equations, beginning with the work by Yulin Zhou and Boling Guo in the early 1980s and including most of the work done by this Chinese group led by Zhou and Guo since. The book focuses on aspects such as the existence of weak solutions in multi dimensions, existence and uniqueness of smooth solutions in one dimension, relations with harmonic map heat flows, partial regularity and long time behaviors. The book is a valuable reference book for those who are interested in partial differential equations, geometric analysis and mathematical physics. It may also be used as an advanced textbook by graduate students in these fields.

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.

Computational Protein Design

Author : Ilan Samish
Publisher : Humana
ISBN 13 : 9781493966356
Total Pages : 0 pages
Book Rating : 4.9/5 (663 download)

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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.

Encyclopedia of Bioinformatics and Computational Biology

Author :
Publisher : Elsevier
ISBN 13 : 0128114320
Total Pages : 3421 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Encyclopedia of Bioinformatics and Computational Biology by :

Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Research in Computational Molecular Biology

Author : Martin Vingron
Publisher : Springer
ISBN 13 : 3540788395
Total Pages : 495 pages
Book Rating : 4.5/5 (47 download)

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Book Synopsis Research in Computational Molecular Biology by : Martin Vingron

Download or read book Research in Computational Molecular Biology written by Martin Vingron and published by Springer. This book was released on 2008-04-03 with total page 495 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2008. It presents current issues in algorithmic, theoretical, and experimental bioinformatics.

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Author : Adam Liwo
Publisher : Springer Science & Business Media
ISBN 13 : 3642285546
Total Pages : 809 pages
Book Rating : 4.6/5 (422 download)

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Book Synopsis Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes by : Adam Liwo

Download or read book Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes written by Adam Liwo and published by Springer Science & Business Media. This book was released on 2013-07-17 with total page 809 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.

Parallel Computing for Bioinformatics and Computational Biology

Author : Albert Y. Zomaya
Publisher : John Wiley & Sons
ISBN 13 : 0471718483
Total Pages : 817 pages
Book Rating : 4.4/5 (717 download)

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Book Synopsis Parallel Computing for Bioinformatics and Computational Biology by : Albert Y. Zomaya

Download or read book Parallel Computing for Bioinformatics and Computational Biology written by Albert Y. Zomaya and published by John Wiley & Sons. This book was released on 2006-04-21 with total page 817 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discover how to streamline complex bioinformatics applications with parallel computing This publication enables readers to handle more complex bioinformatics applications and larger and richer data sets. As the editor clearly shows, using powerful parallel computing tools can lead to significant breakthroughs in deciphering genomes, understanding genetic disease, designing customized drug therapies, and understanding evolution. A broad range of bioinformatics applications is covered with demonstrations on how each one can be parallelized to improve performance and gain faster rates of computation. Current parallel computing techniques and technologies are examined, including distributed computing and grid computing. Readers are provided with a mixture of algorithms, experiments, and simulations that provide not only qualitative but also quantitative insights into the dynamic field of bioinformatics. Parallel Computing for Bioinformatics and Computational Biology is a contributed work that serves as a repository of case studies, collectively demonstrating how parallel computing streamlines difficult problems in bioinformatics and produces better results. Each of the chapters is authored by an established expert in the field and carefully edited to ensure a consistent approach and high standard throughout the publication. The work is organized into five parts: * Algorithms and models * Sequence analysis and microarrays * Phylogenetics * Protein folding * Platforms and enabling technologies Researchers, educators, and students in the field of bioinformatics will discover how high-performance computing can enable them to handle more complex data sets, gain deeper insights, and make new discoveries.

Computational Structural Biology: Methods And Applications

Author : Torsten Schwede
Publisher : World Scientific
ISBN 13 : 9814472417
Total Pages : 790 pages
Book Rating : 4.8/5 (144 download)

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Book Synopsis Computational Structural Biology: Methods And Applications by : Torsten Schwede

Download or read book Computational Structural Biology: Methods And Applications written by Torsten Schwede and published by World Scientific. This book was released on 2008-05-02 with total page 790 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational structural biology has made tremendous progress over the last two decades, and this book provides a recent and broad overview of such computational methods in structural biology. It covers the impact of computational structural biology on protein structure prediction methods, macromolecular function and protein design, and key methods in drug discovery. It also addresses the computational challenges of experimental approaches in structural biology. In addition to reviewing the current state of computational structural biology, each chapter ends with a brief, visionary discussion on the future outlook, whereby the main challenges for the coming years are elucidated. Written by an international panel of expert contributors, this book can serve as a reference manual for students and practitioners alike.

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.

Algorithms in Structural Molecular Biology

Author : Bruce R. Donald
Publisher : MIT Press
ISBN 13 : 0262548798
Total Pages : 497 pages
Book Rating : 4.2/5 (625 download)

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Book Synopsis Algorithms in Structural Molecular Biology by : Bruce R. Donald

Download or read book Algorithms in Structural Molecular Biology written by Bruce R. Donald and published by MIT Press. This book was released on 2023-08-15 with total page 497 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

Algorithms and Methods in Structural Bioinformatics

Author : Nurit Haspel
Publisher : Springer Nature
ISBN 13 : 303105914X
Total Pages : 120 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Algorithms and Methods in Structural Bioinformatics by : Nurit Haspel

Download or read book Algorithms and Methods in Structural Bioinformatics written by Nurit Haspel and published by Springer Nature. This book was released on 2022-09-01 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-dimensional structure and function of molecules present many challenges and opportunities for developing an understanding of biological systems. With the increasing availability of molecular structures and the advancing accuracy of structure predictions and molecular simulations, the space for algorithmic advancement on many analytical and predictive problems is both broad and deep. To support this field, a rich set of methods and algorithms are available, addressing a variety of important problems such as protein-protein interactions, the effect of mutations on protein structure and function, and protein structure determination. Despite recent advancements in the field, in particular in protein folding with the development of AlphaFold, many problems still remain unsolved. In this book we focus on a number of topics in Structural Bioinformatics: Cryo-EM structural detection, protein conformational exploration, elucidation of molecular binding surface using geometry, the effect of mutations, insertions and deletions on protein structural stability, and protein-ligand binding.

Distance Geometry

Author : Antonio Mucherino
Publisher : Springer Science & Business Media
ISBN 13 : 1461451280
Total Pages : 436 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Distance Geometry by : Antonio Mucherino

Download or read book Distance Geometry written by Antonio Mucherino and published by Springer Science & Business Media. This book was released on 2012-12-22 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of research surveys on the Distance Geometry Problem (DGP) and its applications. It will be divided into three parts: Theory, Methods and Applications. Each part will contain at least one survey and several research papers. The first part, Theory, will deal with theoretical aspects of the DGP, including a new class of problems and the study of its complexities as well as the relation between DGP and other related topics, such as: distance matrix theory, Euclidean distance matrix completion problem, multispherical structure of distance matrices, distance geometry and geometric algebra, algebraic distance geometry theory, visualization of K-dimensional structures in the plane, graph rigidity, and theory of discretizable DGP: symmetry and complexity. The second part, Methods, will discuss mathematical and computational properties of methods developed to the problems considered in the first chapter including continuous methods (based on Gaussian and hyperbolic smoothing, difference of convex functions, semidefinite programming, branch-and-bound), discrete methods (based on branch-and-prune, geometric build-up, graph rigidity), and also heuristics methods (based on simulated annealing, genetic algorithms, tabu search, variable neighborhood search). Applications will comprise the third part and will consider applications of DGP to NMR structure calculation, rational drug design, molecular dynamics simulations, graph drawing and sensor network localization. This volume will be the first edited book on distance geometry and applications. The editors are in correspondence with the major contributors to the field of distance geometry, including important research centers in molecular biology such as Institut Pasteur in Paris.

Bio-inspired Computing: Theories and Applications

Author : Linqiang Pan
Publisher : Springer Nature
ISBN 13 : 981153425X
Total Pages : 797 pages
Book Rating : 4.8/5 (115 download)

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Book Synopsis Bio-inspired Computing: Theories and Applications by : Linqiang Pan

Download or read book Bio-inspired Computing: Theories and Applications written by Linqiang Pan and published by Springer Nature. This book was released on 2020-04-01 with total page 797 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two-volume set (CCIS 1159 and CCIS 1160) constitutes the proceedings of the 14th International Conference on Bio-inspired Computing: Theories and Applications, BIC-TA 2019, held in Zhengzhou, China, in November 2019. The 121 full papers presented in both volumes were selected from 197 submissions. The papers are organized according to the topical headings: evolutionary computation and swarm intelligence; bioinformatics and systems biology; complex networks; DNA and molecular computing; neural networks and articial intelligence.