Algorithms In Structural Molecular Biology

Algorithms in Structural Molecular Biology

• Author : Bruce R. Donald
• Publisher : National Geographic Books
• File Size : 17,9 Mb
• Release Date : 2011-06-01
• Genre: Science
• Pages : 0
• ISBN 10 : 9780262015592

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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 in Structural Molecular Biology

• Author : Bruce R. Donald
• Publisher : MIT Press
• File Size : 19,5 Mb
• Release Date : 2011-06-01
• Genre: Science
• Pages : 497
• ISBN 10 : 9780262297844

Download Algorithms in Structural Molecular Biology Book in PDF and ePub

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.

Structural Bioinformatics

• Author : Forbes J. Burkowski
• Publisher : CRC Press
• File Size : 16,9 Mb
• Release Date : 2008-10-30
• Genre: Science
• Pages : 429
• ISBN 10 : 9781420011791

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The Beauty of Protein Structures and the Mathematics behind Structural Bioinformatics Providing the framework for a one-semester undergraduate course, Structural Bioinformatics: An Algorithmic Approach shows how to apply key algorithms to solve problems related to macromolecular structure. Helps Students Go Further in Their Study of Structural Biology Following some introductory material in the first few chapters, the text solves the longest common subsequence problem using dynamic programming and explains the science models for the Nussinov and MFOLD algorithms. It then reviews sequence alignment, along with the basic mathematical calculations needed for measuring the geometric properties of macromolecules. After looking at how coordinate transformations facilitate the translation and rotation of molecules in a 3D space, the author introduces structural comparison techniques, superposition algorithms, and algorithms that compare relationships within a protein. The final chapter explores how regression and classification are becoming more useful in protein analysis and drug design. At the Crossroads of Biology, Mathematics, and Computer Science Connecting biology, mathematics, and computer science, this practical text presents various bioinformatics topics and problems within a scientific methodology that emphasizes nature (the source of empirical observations), science (the mathematical modeling of the natural process), and computation (the science of calculating predictions and mathematical objects based on mathematical models).

Novel Algorithms for Structural Molecular Biology and Proteomics

• Author : Ryan Howard Lilien
• Publisher : Unknown
• File Size : 6,5 Mb
• Release Date : 2004
• Genre: Computational biology
• Pages : 604
• ISBN 10 : OCLC:77960861

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Algorithms in Computational Molecular Biology

• Author : Mourad Elloumi
• Publisher : John Wiley & Sons
• File Size : 16,7 Mb
• Release Date : 2011-04-04
• Genre: Science
• Pages : 1080
• ISBN 10 : 9781118101988

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This book represents the most comprehensive and up-to-date collection of information on the topic of computational molecular biology. Bringing the most recent research into the forefront of discussion, Algorithms in Computational Molecular Biology studies the most important and useful algorithms currently being used in the field, and provides related problems. It also succeeds where other titles have failed, in offering a wide range of information from the introductory fundamentals right up to the latest, most advanced levels of study.

Research in Computational Molecular Biology

• Author : Minghua Deng
• Publisher : Springer
• File Size : 15,5 Mb
• Release Date : 2013-03-12
• Genre: Computers
• Pages : 346
• ISBN 10 : 9783642371950

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This book constitutes the refereed proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, held in Beijing, China, in April 2013. The 32 revised full papers were carefully reviewed and selected from 167 submissions. The papers cover a wide range of topics including molecular sequence analysis; genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; epigenomics; metagenomics; population, statistical genetics; systems biology; computational proteomics; computational structural biology; imaging; large-scale data management.

Introduction to Protein Structure Prediction

• Author : Huzefa Rangwala
• Publisher : John Wiley & Sons
• File Size : 13,9 Mb
• Release Date : 2011-03-16
• Genre: Science
• Pages : 520
• ISBN 10 : 111809946X

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A look at the methods and algorithms used to predict proteinstructure A thorough knowledge of the function and structure of proteinsis critical for the advancement of biology and the life sciences aswell as the development of better drugs, higher-yield crops, andeven synthetic bio-fuels. To that end, this reference sheds lighton the methods used for protein structure prediction and revealsthe key applications of modeled structures. This indispensable bookcovers the applications of modeled protein structures and unravelsthe relationship between pure sequence information andthree-dimensional structure, which continues to be one of thegreatest challenges in molecular biology. With this resource, readers will find an all-encompassingexamination of the problems, methods, tools, servers, databases,and applications of protein structure prediction and they willacquire unique insight into the future applications of the modeledprotein structures. The book begins with a thorough introduction tothe protein structure prediction problem and is divided into fourthemes: a background on structure prediction, the prediction ofstructural elements, tertiary structure prediction, and functionalinsights. Within those four sections, the following topics arecovered: Databases and resources that are commonly used for proteinstructure prediction The structure prediction flagship assessment (CASP) and theprotein structure initiative (PSI) Definitions of recurring substructures and the computationalapproaches used for solving sequence problems Difficulties with contact map prediction and how sophisticatedmachine learning methods can solve those problems Structure prediction methods that rely on homology modeling,threading, and fragment assembly Hybrid methods that achieve high-resolution proteinstructures Parts of the protein structure that may be conserved and usedto interact with other biomolecules How the loop prediction problem can be used for refinement ofthe modeled structures The comput

Algorithms and Methods in Structural Bioinformatics

• Author : Nurit Haspel
• Publisher : Springer Nature
• File Size : 15,6 Mb
• Release Date : 2022-09-01
• Genre: Science
• Pages : 120
• ISBN 10 : 9783031059148

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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.

Bioinformatics Algorithms

• Author : Ion Mandoiu
• Publisher : John Wiley & Sons
• File Size : 7,7 Mb
• Release Date : 2008-02-25
• Genre: Computers
• Pages : 528
• ISBN 10 : 9780470097731

Download Bioinformatics Algorithms Book in PDF and ePub

Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers: General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.

Algorithmic Foundations of Robotics VI

• Author : Michael Erdmann
• Publisher : Springer Science & Business Media
• File Size : 11,5 Mb
• Release Date : 2005-06-23
• Genre: Technology & Engineering
• Pages : 480
• ISBN 10 : 3540257284

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Robot algorithms are abstractions of computational processes that control or reason about motion and perception in the physical world. Because actions in the physical world are subject to physical laws and geometric constraints, the design and analysis of robot algorithms raise a unique combination of questions in control theory, computational and differential geometry, and computer science. Algorithms serve as a unifying theme in the multi-disciplinary field of robotics. This volume consists of selected contributions to the sixth Workshop on the Algorithmic Foundations of Robotics. This is a highly competitive meeting of experts in the field of algorithmic issues related to robotics and automation.

Research in Computational Molecular Biology

• Author : Teresa M. Przytycka
• Publisher : Springer
• File Size : 16,6 Mb
• Release Date : 2015-03-25
• Genre: Computers
• Pages : 368
• ISBN 10 : 9783319167060

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This book constitutes the refereed proceedings of the 19th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2015, held in Warsaw, Poland, in April 2015. The 36 extended abstracts were carefully reviewed and selected from 170 submissions. They report on original research in all areas of computational molecular biology and bioinformatics.

Structural Matching Algorithms in Molecular Biology

• Author : Daniel Fischer
• Publisher : Unknown
• File Size : 10,7 Mb
• Release Date : 1993
• Genre: Uncategoriezed
• Pages : 143
• ISBN 10 : OCLC:884945627

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Advances in Protein Molecular and Structural Biology Methods

• Author : Timir Tripathi
• Publisher : Academic Press
• File Size : 11,5 Mb
• Release Date : 2022-01-14
• Genre: Science
• Pages : 714
• ISBN 10 : 9780323902656

Download Advances in Protein Molecular and Structural Biology Methods Book in PDF and ePub

Advances in Protein Molecular and Structural Biology Methods offers a complete overview of the latest tools and methods applicable to the study of proteins at the molecular and structural level. The book begins with sections exploring tools to optimize recombinant protein expression and biophysical techniques such as fluorescence spectroscopy, NMR, mass spectrometry, cryo-electron microscopy, and X-ray crystallography. It then moves towards computational approaches, considering structural bioinformatics, molecular dynamics simulations, and deep machine learning technologies. The book also covers methods applied to intrinsically disordered proteins (IDPs)followed by chapters on protein interaction networks, protein function, and protein design and engineering. It provides researchers with an extensive toolkit of methods and techniques to draw from when conducting their own experimental work, taking them from foundational concepts to practical application. Presents a thorough overview of the latest and emerging methods and technologies for protein study Explores biophysical techniques, including nuclear magnetic resonance, X-ray crystallography, and cryo-electron microscopy Includes computational and machine learning methods Features a section dedicated to tools and techniques specific to studying intrinsically disordered proteins

Algorithms in Bioinformatics

• Author : Rita Casadio
• Publisher : Springer Science & Business Media
• File Size : 11,8 Mb
• Release Date : 2005-09-27
• Genre: Computers
• Pages : 446
• ISBN 10 : 9783540290087

Download Algorithms in Bioinformatics Book in PDF and ePub

This book constitutes the refereed proceedings of the 5th International Workshop on Algorithms in Bioinformatics, WABI 2005, held in Mallorca, Spain, in September 2005 as part of the ALGO 2005 conference meetings. The 34 revised full papers presented were carefully reviewed and selected from 95 submissions. All current issues of algorithms in bioinformatics are addressed with special focus on statistical and probabilistic algorithms in the field of molecular and structural biology. The papers are organized in topical sections on expression (hybrid methods and time patterns), phylogeny (quartets, tree reconciliation, clades and haplotypes), networks, genome rearrangements (transposition model and other models), sequences (strings, multi-alignment and clustering, clustering and representation), and structure (threading and folding).

Introduction to Protein Structure Prediction

• Author : Huzefa Rangwala
• Publisher : Wiley
• File Size : 20,5 Mb
• Release Date : 2010-12-28
• Genre: Science
• Pages : 516
• ISBN 10 : 0470470593

Download Introduction to Protein Structure Prediction Book in PDF and ePub

A look at the methods and algorithms used to predict protein structure A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure prediction The structure prediction flagship assessment (CASP) and the protein structure initiative (PSI) Definitions of recurring substructures and the computational approaches used for solving sequence problems Difficulties with contact map prediction and how sophisticated machine learning methods can solve those problems Structure prediction methods that rely on homology modeling, threading, and fragment assembly Hybrid methods that achieve high-resolution protein structures Parts of the protein structure that may be conserved and used to interact with other biomolecules How the loop prediction problem can be used for refinement of the mo