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Download or read book Lecture Notes on Computational Structural Biology written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author: Zhijun Wu
Publisher: World Scientific
Published: 2008
Total Pages: 243
ISBN-13: 9812814787
DOWNLOAD EBOOK1. Introduction. 1.1. Protein structure. 1.2. Structure determination. 1.3. Dynamics simulation. 1.4. The myth of protein folding -- 2. X-ray crystallography computing. 2.1. The phase problem. 2.2. Least squares solutions. 2.3. Entropy maximization. 2.4. Indirect methods -- 3. NMR structure determination. 3.1. Nuclear magnetic resonance. 3.2. Distance geometry. 3.3. Distance-based modeling. 3.4. Structural analysis -- 4. Potential energy minimization. 4.1. Potential energy function. 4.2. Local optimization. 4.3. Global optimization. 4.4. Energy transformation -- 5. Molecular dynamics simulation. 5.1. Equations of motion. 5.2. Initial-value problem. 5.3. Boundary-value problem. 5.4. Normal mode analysis -- 6. Knowledge-based protein modeling. 6.1. Sequence/structural alignment. 6.2. Fold recognition/inverse folding. 6.3. Knowledge-based structural refinement. 6.4. Structural computing and beyond
Download or read book Lecture Notes on Computational Structural Biology written by Zhijun Wu and published by World Scientific. This book was released on 2008 with total page 243 pages. Available in PDF, EPUB and Kindle. Book excerpt: 1. Introduction. 1.1. Protein structure. 1.2. Structure determination. 1.3. Dynamics simulation. 1.4. The myth of protein folding -- 2. X-ray crystallography computing. 2.1. The phase problem. 2.2. Least squares solutions. 2.3. Entropy maximization. 2.4. Indirect methods -- 3. NMR structure determination. 3.1. Nuclear magnetic resonance. 3.2. Distance geometry. 3.3. Distance-based modeling. 3.4. Structural analysis -- 4. Potential energy minimization. 4.1. Potential energy function. 4.2. Local optimization. 4.3. Global optimization. 4.4. Energy transformation -- 5. Molecular dynamics simulation. 5.1. Equations of motion. 5.2. Initial-value problem. 5.3. Boundary-value problem. 5.4. Normal mode analysis -- 6. Knowledge-based protein modeling. 6.1. Sequence/structural alignment. 6.2. Fold recognition/inverse folding. 6.3. Knowledge-based structural refinement. 6.4. Structural computing and beyond
Author: Torsten Schwede
Publisher: World Scientific
Published: 2008
Total Pages: 790
ISBN-13: 9812778780
DOWNLOAD EBOOKThis 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.
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.
Author: Rui Jiang
Publisher: Springer Science & Business Media
Published: 2013-11-26
Total Pages: 412
ISBN-13: 3642389511
DOWNLOAD EBOOKThis book outlines 11 courses and 15 research topics in bioinformatics, based on curriculums and talks in a graduate summer school on bioinformatics that was held in Tsinghua University. The courses include: Basics for Bioinformatics, Basic Statistics for Bioinformatics, Topics in Computational Genomics, Statistical Methods in Bioinformatics, Algorithms in Computational Biology, Multivariate Statistical Methods in Bioinformatics Research, Association Analysis for Human Diseases: Methods and Examples, Data Mining and Knowledge Discovery Methods with Case Examples, Applied Bioinformatics Tools, Foundations for the Study of Structure and Function of Proteins, Computational Systems Biology Approaches for Deciphering Traditional Chinese Medicine, and Advanced Topics in Bioinformatics and Computational Biology. This book can serve as not only a primer for beginners in bioinformatics, but also a highly summarized yet systematic reference book for researchers in this field. Rui Jiang and Xuegong Zhang are both professors at the Department of Automation, Tsinghua University, China. Professor Michael Q. Zhang works at the Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Download or read book Basics of Bioinformatics written by Rui Jiang and published by Springer Science & Business Media. This book was released on 2013-11-26 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book outlines 11 courses and 15 research topics in bioinformatics, based on curriculums and talks in a graduate summer school on bioinformatics that was held in Tsinghua University. The courses include: Basics for Bioinformatics, Basic Statistics for Bioinformatics, Topics in Computational Genomics, Statistical Methods in Bioinformatics, Algorithms in Computational Biology, Multivariate Statistical Methods in Bioinformatics Research, Association Analysis for Human Diseases: Methods and Examples, Data Mining and Knowledge Discovery Methods with Case Examples, Applied Bioinformatics Tools, Foundations for the Study of Structure and Function of Proteins, Computational Systems Biology Approaches for Deciphering Traditional Chinese Medicine, and Advanced Topics in Bioinformatics and Computational Biology. This book can serve as not only a primer for beginners in bioinformatics, but also a highly summarized yet systematic reference book for researchers in this field. Rui Jiang and Xuegong Zhang are both professors at the Department of Automation, Tsinghua University, China. Professor Michael Q. Zhang works at the Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Author: Bruce R. Donald
Publisher: MIT Press
Published: 2023-08-15
Total Pages: 497
ISBN-13: 0262548798
DOWNLOAD EBOOKAn 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.
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.
Download or read book Computational Structural Biology written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author: Forbes J. Burkowski
Publisher: CRC Press
Published: 2008-10-30
Total Pages: 444
ISBN-13: 1420011790
DOWNLOAD EBOOKThe Beauty of Protein Structures and the Mathematics behind Structural BioinformaticsProviding 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 Biolog
Download or read book Structural Bioinformatics written by Forbes J. Burkowski and published by CRC Press. This book was released on 2008-10-30 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Beauty of Protein Structures and the Mathematics behind Structural BioinformaticsProviding 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 Biolog
Author: Gordon Plotkin
Publisher: Springer Science & Business Media
Published: 2006-11-27
Total Pages: 253
ISBN-13: 3540457798
DOWNLOAD EBOOKThe 5th Transactions on Computational Systems Biology volume, edited by Gordon Plotkin, features carefully selected and enhanced contributions initially presented at the 2005 IEEE International Conference on Granular Computing. The 9 papers selected for this special issue discuss various aspects of computational methods, algorithm and techniques in bioinformatics such as gene expression analysis, biomedical literature mining and natural language processing, protein structure prediction, biological database management and biomedical information retrieval.
Download or read book Transactions on Computational Systems Biology VI written by Gordon Plotkin and published by Springer Science & Business Media. This book was released on 2006-11-27 with total page 253 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 5th Transactions on Computational Systems Biology volume, edited by Gordon Plotkin, features carefully selected and enhanced contributions initially presented at the 2005 IEEE International Conference on Granular Computing. The 9 papers selected for this special issue discuss various aspects of computational methods, algorithm and techniques in bioinformatics such as gene expression analysis, biomedical literature mining and natural language processing, protein structure prediction, biological database management and biomedical information retrieval.
Author: Alexander Zelikovsky
Publisher: Springer Science & Business Media
Published: 2005-11-04
Total Pages: 161
ISBN-13: 3540294015
DOWNLOAD EBOOKThe LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This second volume of the Transactions on Computational Systems Biology is devoted to considerably extended versions of selected papers presented at the International Workshop on Bioinformatics Research and Applications (IWBRA 2005), part of the International Conference on Computational Science (ICCS 2005), which took place at Emory University, Atlanta, Georgia, USA, in May 2005. The ten papers selected for the special issue cover a wide range of bioinformatics research such as problems in RNA structure prediction, coding schemes and structural alphabets for protein structure prediction, novel techniques for efficient gene transfer in phylogenetic networks, practical algorithms minimizing recombinations in pedigree phasing, parallel implementation in Open MP for finding the corresponding shortest edit distance between two signed gene permutations, and bioinformatics problems in DNA microarrays.
Download or read book Transactions on Computational Systems Biology II written by Alexander Zelikovsky and published by Springer Science & Business Media. This book was released on 2005-11-04 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This second volume of the Transactions on Computational Systems Biology is devoted to considerably extended versions of selected papers presented at the International Workshop on Bioinformatics Research and Applications (IWBRA 2005), part of the International Conference on Computational Science (ICCS 2005), which took place at Emory University, Atlanta, Georgia, USA, in May 2005. The ten papers selected for the special issue cover a wide range of bioinformatics research such as problems in RNA structure prediction, coding schemes and structural alphabets for protein structure prediction, novel techniques for efficient gene transfer in phylogenetic networks, practical algorithms minimizing recombinations in pedigree phasing, parallel implementation in Open MP for finding the corresponding shortest edit distance between two signed gene permutations, and bioinformatics problems in DNA microarrays.
Author: Daniel Figueiredo
Publisher: Springer
Published: 2017-05-26
Total Pages: 184
ISBN-13: 3319581635
DOWNLOAD EBOOKThis book constitutes the proceedings of the 4th InternationalConference on Algorithms for Computational Biology, AlCoB 2017, held in Aveiro, Portugal, in June 2017. The 10 full papers presented together with 2 invited papers were carefully reviewed and selected from 24 submissions. They are organized in the following topical sections: Graph Algorithms for Computational Biology; Phylogenetics; and Sequence Analysis and Other Biological Processes.
Download or read book Algorithms for Computational Biology written by Daniel Figueiredo and published by Springer. This book was released on 2017-05-26 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 4th InternationalConference on Algorithms for Computational Biology, AlCoB 2017, held in Aveiro, Portugal, in June 2017. The 10 full papers presented together with 2 invited papers were carefully reviewed and selected from 24 submissions. They are organized in the following topical sections: Graph Algorithms for Computational Biology; Phylogenetics; and Sequence Analysis and Other Biological Processes.
