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Author: P. Therese Lang Publisher: ISBN: Category : Languages : en Pages : 538
Book Description
The aim of this thesis was to improve computational methods for structure based drug design, particularly for RNA targets. For the first portion, we present a critical evaluation of various computational drug design algorithms for their ability to predict experimental binding poses and rank libraries of small molecules against protein targets. In particular, we characterize the strengths and weaknesses of the ligand sampling method for the DOCK suite of programs. In the second portion of the thesis, we apply the lessons learned from protein targets to the disruption of protein-RNA interactions critical to the life cycle of the HIV virus. As a class, RNA historically has presented a difficult computational challenge both due to its highly localized charge and flexibility. Therefore, we have extended protocols and added new protocols in existing software packages such as DOCK and AMBER to predict experimental binding poses, once again validating our results using experimental data. Finally, we apply these protocols both to develop libraries of small molecules against druggable RNA targets and to establish a fragment-based library designed to find new scaffolds for RNA.
Author: P. Therese Lang Publisher: ISBN: Category : Languages : en Pages : 538
Book Description
The aim of this thesis was to improve computational methods for structure based drug design, particularly for RNA targets. For the first portion, we present a critical evaluation of various computational drug design algorithms for their ability to predict experimental binding poses and rank libraries of small molecules against protein targets. In particular, we characterize the strengths and weaknesses of the ligand sampling method for the DOCK suite of programs. In the second portion of the thesis, we apply the lessons learned from protein targets to the disruption of protein-RNA interactions critical to the life cycle of the HIV virus. As a class, RNA historically has presented a difficult computational challenge both due to its highly localized charge and flexibility. Therefore, we have extended protocols and added new protocols in existing software packages such as DOCK and AMBER to predict experimental binding poses, once again validating our results using experimental data. Finally, we apply these protocols both to develop libraries of small molecules against druggable RNA targets and to establish a fragment-based library designed to find new scaffolds for RNA.
Author: S.L. Salzberg Publisher: Elsevier ISBN: 0080860931 Category : Computers Languages : en Pages : 399
Book Description
Computational biology is a rapidly expanding field, and the number and variety of computational methods used for DNA and protein sequence analysis is growing every day. These algorithms are extremely valuable to biotechnology companies and to researchers and teachers in universities. This book explains the latest computer technology for analyzing DNA, RNA, and protein sequences. Clear and easy to follow, designed specifically for the non-computer scientist, it will help biologists make better choices on which algorithm to use. New techniques and demonstrations are elucidated, as are state-of-the-art problems, and more advanced material on the latest algorithms. The primary audience for this volume are molecular biologists working either in biotechnology companies or academic research environments, individual researchers and the institutions they work for, and students. Any biologist who relies on computers should want this book. A secondary audience will be computer scientists developing techniques with applications in biology. An excellent reference for leading techniques, it will also help introduce computer scientists to the biology problems. This is an outstanding work which will be ideal for the increasing number of scientists moving into computational biology.
Author: Mourad Elloumi Publisher: John Wiley & Sons ISBN: 1119078857 Category : Technology & Engineering Languages : en Pages : 655
Book Description
A comprehensive overview of high-performance pattern recognition techniques and approaches to Computational Molecular Biology This book surveys the developments of techniques and approaches on pattern recognition related to Computational Molecular Biology. Providing a broad coverage of the field, the authors cover fundamental and technical information on these techniques and approaches, as well as discussing their related problems. The text consists of twenty nine chapters, organized into seven parts: Pattern Recognition in Sequences, Pattern Recognition in Secondary Structures, Pattern Recognition in Tertiary Structures, Pattern Recognition in Quaternary Structures, Pattern Recognition in Microarrays, Pattern Recognition in Phylogenetic Trees, and Pattern Recognition in Biological Networks. Surveys the development of techniques and approaches on pattern recognition in biomolecular data Discusses pattern recognition in primary, secondary, tertiary and quaternary structures, as well as microarrays, phylogenetic trees and biological networks Includes case studies and examples to further illustrate the concepts discussed in the book Pattern Recognition in Computational Molecular Biology: Techniques and Approaches is a reference for practitioners and professional researches in Computer Science, Life Science, and Mathematics. This book also serves as a supplementary reading for graduate students and young researches interested in Computational Molecular Biology.
Author: National Research Council Publisher: National Academies Press ISBN: 0309062284 Category : Computers Languages : en Pages : 186
Book Description
In much of biology, the search for understanding the relation between structure and function is now taking place at the macromolecular level. Proteins, nucleic acids, and polysaccharides are macromolecule--polymers formed from families of simpler subunits. Because of their size and complexity, the polymers are capable of both inter- and intramolecular interactions. These interactions confer upon the polymers distinctive three-dimensional shapes. These tertiary configurations, in turn, determine the function of the macromolecule. Computers have become so inextricably involved in empirical studies of three-dimensional macromolecular structure that mathematical modeling, or theory, and experimental approaches are interrelated aspects of a single enterprise.
Author: Jirí Šponer Publisher: Springer Science & Business Media ISBN: 1402048513 Category : Science Languages : en Pages : 638
Book Description
This book integrates modern computational studies of nucleic acids, ranging from advanced electronic structure quantum chemical calculations through explicit solvent molecular dynamics (MD) simulations up to mesoscopic modelling, with the main focus given to the MD field. It gives an equal emphasis to the leading methods and applications while successes as well as pitfalls of the computational techniques are discussed.
Author: M Michael Gromiha Publisher: World Scientific ISBN: 9811211884 Category : Science Languages : en Pages : 424
Book Description
This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.
Author: Publisher: Academic Press ISBN: 0128016183 Category : Science Languages : en Pages : 449
Book Description
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers computational prediction RNA structure and dynamics, including such topics as computational modeling of RNA secondary and tertiary structures, riboswitch dynamics, and ion-RNA, ligand-RNA and DNA-RNA interactions. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers computational methods and applications in RNA structure and dynamics Contains chapters with emerging topics such as RNA structure prediction, riboswitch dynamics and thermodynamics, and effects of ions and ligands.
Author: Xin Lai Publisher: Humana Press ISBN: 9781493989812 Category : Science Languages : en Pages : 390
Book Description
This volume details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Computational Biology of Non-Coding RNA: Methods and Protocols aims to provide a state-of-the-art collection of computational methods and approaches that will be of value to researchers interested in ncRNA field.
Author: P. Therese Lang
Author: P. Therese Lang
Author: S.L. Salzberg
Author: Mourad Elloumi
Author: National Research Council
Author: Jirí Šponer
Author: M Michael Gromiha
Author: 
Author: Daniel James Battle
Author: Efrat Kligun
Author: Xin Lai