Computational Biology And Chemistry

Author : Payam Behzadi,Nicola Bernabò
Publisher : BoD – Books on Demand
Page : 151 pages
File Size : 40,5 Mb
Release : 2020-12
Category : Bioinformatics
ISBN : 9781789853667

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Computational Biology and Chemistry by Payam Behzadi,Nicola Bernabò Pdf

The use of computers and software tools in biochemistry (biology) has led to a deep revolution in basic sciences and medicine. Bioinformatics and systems biology are the direct results of this revolution. With the involvement of computers, software tools, and internet services in scientific disciplines comprising biology and chemistry, new terms, technologies, and methodologies appeared and established. Bioinformatic software tools, versatile databases, and easy internet access resulted in the occurrence of computational biology and chemistry. Today, we have new types of surveys and laboratories including "in silico studies" and "dry labs" in which bioinformaticians conduct their investigations to gain invaluable outcomes. These features have led to 3-dimensioned illustrations of different molecules and complexes to get a better understanding of nature.

Author : Sonsoles Martín-Santamaría
Publisher : Royal Society of Chemistry
Page : 392 pages
File Size : 53,7 Mb
Release : 2017-11-01
Category : Science
ISBN : 9781782627005

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Computational Tools for Chemical Biology by Sonsoles Martín-Santamaría Pdf

This book offers a fresh perspective on how computational tools can aid the chemical biology research community and drive new research.

Author : Tanmoy Chakraborty,Prabhat Ranjan,Anand Pandey
Publisher : CRC Press
Page : 394 pages
File Size : 47,8 Mb
Release : 2017-10-03
Category : Science
ISBN : 9781351800365

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Computational Chemistry Methodology in Structural Biology and Materials Sciences by Tanmoy Chakraborty,Prabhat Ranjan,Anand Pandey Pdf

Computational Chemistry Methodology in Structural Biology and Materials Sciences provides a selection of new research in theoretical and experimental chemistry, focusing on topics in the materials science and biological activity. Part 1, on Computational Chemistry Methodology in Biological Activity, of the book emphasizes presents new developments in the domain of theoretical and computational chemistry and its applications to bioactive molecules. It looks at various aspects of density functional theory and other issues. Part 2, on Computational Chemistry Methodology in Materials Science, presents informative new research on computational chemistry as applied to materials science. The wide range of topics regarding the application of theoretical and experimental chemistry and materials science and biological domain will be valuable in the context of addressing contemporary research problems.

Author : Tao Jiang,Ying Xu,Michael Q. Zhang
Publisher : MIT Press
Page : 570 pages
File Size : 45,8 Mb
Release : 2002
Category : Computers
ISBN : 0262100924

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Current Topics in Computational Molecular Biology by Tao Jiang,Ying Xu,Michael Q. Zhang Pdf

A survey of current topics in computational molecular biology. Computational molecular biology, or bioinformatics, draws on the disciplines of biology, mathematics, statistics, physics, chemistry, computer science, and engineering. It provides the computational support for functional genomics, which links the behavior of cells, organisms, and populations to the information encoded in the genomes, as well as for structural genomics. At the heart of all large-scale and high-throughput biotechnologies, it has a growing impact on health and medicine. This survey of computational molecular biology covers traditional topics such as protein structure modeling and sequence alignment, and more recent ones such as expression data analysis and comparative genomics. It combines algorithmic, statistical, database, and AI-based methods for studying biological problems. The book also contains an introductory chapter, as well as one on general statistical modeling and computational techniques in molecular biology. Each chapter presents a self-contained review of a specific subject. Not for sale in China, including Hong Kong.

Author : Jürgen Bajorath
Publisher : Humana Press
Page : 588 pages
File Size : 48,5 Mb
Release : 2010-09-22
Category : Science
ISBN : 1607618389

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Chemoinformatics and Computational Chemical Biology by Jürgen Bajorath Pdf

Over the past years, the chem(o)informatics field has further evolved and new application areas have opened up, for example, in the broadly defined area of chemical biology. In Chemoinformatics and Computational Chemical Biology, leading investigators bring together a detailed series of reviews and methods including, among others, system-directed approaches using small molecules, the design of target-focused compound libraries, the study of molecular selectivity, and the systematic analysis of target-ligand interactions. Furthermore, the book delves into similarity methods, machine learning, probabilistic approaches, fragment-based methods, as well as topics that go beyond the current chemoinformatics spectrum, such as knowledge-based modeling of G protein-coupled receptor structures and computational design of siRNA libraries. As a volume in the highly successful Methods in Molecular BiologyTM series, this collection provides detailed descriptions and implementation advice that are exceedingly relevant for basic researchers and practitioners in this highly interdisciplinary research and development area. Cutting-edge and unambiguous, Chemoinformatics and Computational Chemical Biology serves as an ideal guide for experts and newcomers alike to this vital and dynamic field of study.

Author : Dongqing Wei,Qin Xu,Tangzhen Zhao,Hao Dai
Publisher : Springer
Page : 380 pages
File Size : 42,7 Mb
Release : 2014-11-11
Category : Science
ISBN : 9789401792455

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Advance in Structural Bioinformatics by Dongqing Wei,Qin Xu,Tangzhen Zhao,Hao Dai Pdf

This text examines in detail mathematical and physical modeling, computational methods and systems for obtaining and analyzing biological structures, using pioneering research cases as examples. As such, it emphasizes programming and problem-solving skills. It provides information on structure bioinformatics at various levels, with individual chapters covering introductory to advanced aspects, from fundamental methods and guidelines on acquiring and analyzing genomics and proteomics sequences, the structures of protein, DNA and RNA, to the basics of physical simulations and methods for conformation searches. This book will be of immense value to researchers and students in the fields of bioinformatics, computational biology and chemistry. Dr. Dongqing Wei is a Professor at the Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China. His research interest is in the general area of structural bioinformatics.

Author : Huma M. Lodhi,Stephen H. Muggleton
Publisher : John Wiley & Sons
Page : 435 pages
File Size : 47,6 Mb
Release : 2010-03-25
Category : Computers
ISBN : 9780470556740

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Elements of Computational Systems Biology by Huma M. Lodhi,Stephen H. Muggleton Pdf

Groundbreaking, long-ranging research in this emergent field that enables solutions to complex biological problems Computational systems biology is an emerging discipline that is evolving quickly due to recent advances in biology such as genome sequencing, high-throughput technologies, and the recent development of sophisticated computational methodologies. Elements of Computational Systems Biology is a comprehensive reference covering the computational frameworks and techniques needed to help research scientists and professionals in computer science, biology, chemistry, pharmaceutical science, and physics solve complex biological problems. Written by leading experts in the field, this practical resource gives detailed descriptions of core subjects, including biological network modeling, analysis, and inference; presents a measured introduction to foundational topics like genomics; and describes state-of-the-art software tools for systems biology. Offers a coordinated integrated systems view of defining and applying computational and mathematical tools and methods to solving problems in systems biology Chapters provide a multidisciplinary approach and range from analysis, modeling, prediction, reasoning, inference, and exploration of biological systems to the implications of computational systems biology on drug design and medicine Helps reduce the gap between mathematics and biology by presenting chapters on mathematical models of biological systems Establishes solutions in computer science, biology, chemistry, and physics by presenting an in-depth description of computational methodologies for systems biology Elements of Computational Systems Biology is intended for academic/industry researchers and scientists in computer science, biology, mathematics, chemistry, physics, biotechnology, and pharmaceutical science. It is also accessible to undergraduate and graduate students in machine learning, data mining, bioinformatics, computational biology, and systems biology courses.

Author : Walter Rocchia,Michela Spagnuolo
Publisher : Springer
Page : 311 pages
File Size : 40,5 Mb
Release : 2014-11-29
Category : Science
ISBN : 9783319122113

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Computational Electrostatics for Biological Applications by Walter Rocchia,Michela Spagnuolo Pdf

This book presents established and new approaches to perform calculations of electrostatic interactions at the nanoscale, with particular focus on molecular biology applications. It is based on the proceedings of the Computational Electrostatics for Biological Applications international meeting, which brought together researchers in computational disciplines to discuss and explore diverse methods to improve electrostatic calculations. Fostering an interdisciplinary approach to the description of complex physical and biological problems, this book encompasses contributions originating in the fields of geometry processing, shape modeling, applied mathematics, and computational biology and chemistry. The main topics covered are theoretical and numerical aspects of the solution of the Poisson-Boltzmann equation, surveys and comparison among geometric approaches to the modelling of molecular surfaces and related discretization and computational issues. It also includes a number of contributions addressing applications in biology, biophysics and nanotechnology. The book is primarily intended as a reference for researchers in the computational molecular biology and chemistry fields. As such, it also aims at becoming a key source of information for a wide range of scientists who need to know how modeling and computing at the molecular level may influence the design and interpretation of their experiments.

Author : Christodoulos A. Floudas,Panos M. Pardalos
Publisher : Springer Science & Business Media
Page : 341 pages
File Size : 49,7 Mb
Release : 2013-06-29
Category : Computers
ISBN : 9781475732184

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Optimization in Computational Chemistry and Molecular Biology by Christodoulos A. Floudas,Panos M. Pardalos Pdf

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.

Author : William T. Loging
Publisher : Cambridge University Press
Page : 255 pages
File Size : 49,5 Mb
Release : 2016-03-17
Category : Science
ISBN : 9780521768009

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Bioinformatics and Computational Biology in Drug Discovery and Development by William T. Loging Pdf

A comprehensive overview of the use of computational biology approaches in the drug discovery and development process.

Author : Alexandre Varnek
Publisher : John Wiley & Sons
Page : 488 pages
File Size : 47,6 Mb
Release : 2017-06-22
Category : Science
ISBN : 9781119137986

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Tutorials in Chemoinformatics by Alexandre Varnek Pdf

30 tutorials and more than 100 exercises in chemoinformatics, supported by online software and data sets Chemoinformatics is widely used in both academic and industrial chemical and biochemical research worldwide. Yet, until this unique guide, there were no books offering practical exercises in chemoinformatics methods. Tutorials in Chemoinformatics contains more than 100 exercises in 30 tutorials exploring key topics and methods in the field. It takes an applied approach to the subject with a strong emphasis on problem-solving and computational methodologies. Each tutorial is self-contained and contains exercises for students to work through using a variety of software packages. The majority of the tutorials are divided into three sections devoted to theoretical background, algorithm description and software applications, respectively, with the latter section providing step-by-step software instructions. Throughout, three types of software tools are used: in-house programs developed by the authors, open-source programs and commercial programs which are available for free or at a modest cost to academics. The in-house software and data sets are available on a dedicated companion website. Key topics and methods covered in Tutorials in Chemoinformatics include: Data curation and standardization Development and use of chemical databases Structure encoding by molecular descriptors, text strings and binary fingerprints The design of diverse and focused libraries Chemical data analysis and visualization Structure-property/activity modeling (QSAR/QSPR) Ensemble modeling approaches, including bagging, boosting, stacking and random subspaces 3D pharmacophores modeling and pharmacological profiling using shape analysis Protein-ligand docking Implementation of algorithms in a high-level programming language Tutorials in Chemoinformatics is an ideal supplementary text for advanced undergraduate and graduate courses in chemoinformatics, bioinformatics, computational chemistry, computational biology, medicinal chemistry and biochemistry. It is also a valuable working resource for medicinal chemists, academic researchers and industrial chemists looking to enhance their chemoinformatics skills.

Author : Sadasivan Shankar,Richard Muller,Thom Dunning,Guan Hua Chen
Publisher : Springer Nature
Page : 1344 pages
File Size : 50,8 Mb
Release : 2021-01-25
Category : Technology & Engineering
ISBN : 9783030187781

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Computational Materials, Chemistry, and Biochemistry: From Bold Initiatives to the Last Mile by Sadasivan Shankar,Richard Muller,Thom Dunning,Guan Hua Chen Pdf

This book provides a broad and nuanced overview of the achievements and legacy of Professor William (“Bill”) Goddard in the field of computational materials and molecular science. Leading researchers from around the globe discuss Goddard’s work and its lasting impacts, which can be seen in today’s cutting-edge chemistry, materials science, and biology techniques. Each section of the book closes with an outline of the prospects for future developments. In the course of a career spanning more than 50 years, Goddard’s seminal work has led to dramatic advances in a diverse range of science and engineering fields. Presenting scientific essays and reflections by students, postdoctoral associates, collaborators and colleagues, the book describes the contributions of one of the world’s greatest materials and molecular scientists in the context of theory, experimentation, and applications, and examines his legacy in each area, from conceptualization (the first mile) to developments and extensions aimed at applications, and lastly to de novo design (the last mile). Goddard’s passion for science, his insights, and his ability to actively engage with his collaborators in bold initiatives is a model for us all. As he enters his second half-century of scientific research and education, this book inspires future generations of students and researchers to employ and extend these powerful techniques and insights to tackle today’s critical problems in biology, chemistry, and materials. Examples highlighted in the book include new materials for photocatalysts to convert water and CO2 into fuels, novel catalysts for the highly selective and active catalysis of alkanes to valuable organics, simulating the chemistry in film growth to develop two-dimensional functional films, and predicting ligand–protein binding and activation to enable the design of targeted drugs with minimal side effects.

Author : Aman Chandra Kaushik,Aamir Mehmood,Dong-Qing Wei,Sadia Nawab,Shakti Sahi,Ajay Kumar
Publisher : Royal Society of Chemistry
Page : 281 pages
File Size : 48,5 Mb
Release : 2023-09-08
Category : Science
ISBN : 9781839161629

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Cheminformatics and Bioinformatics at the Interface with Systems Biology by Aman Chandra Kaushik,Aamir Mehmood,Dong-Qing Wei,Sadia Nawab,Shakti Sahi,Ajay Kumar Pdf

Author : Matthias Dehmer,Yongtang Shi,Frank Emmert-Streib
Publisher : John Wiley & Sons
Page : 364 pages
File Size : 41,5 Mb
Release : 2016-12-12
Category : Medical
ISBN : 9783527339587

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Computational Network Analysis with R by Matthias Dehmer,Yongtang Shi,Frank Emmert-Streib Pdf

This new title in the well-established "Quantitative Network Biology" series includes innovative and existing methods for analyzing network data in such areas as network biology and chemoinformatics. With its easy-to-follow introduction to the theoretical background and application-oriented chapters, the book demonstrates that R is a powerful language for statistically analyzing networks and for solving such large-scale phenomena as network sampling and bootstrapping. Written by editors and authors with an excellent track record in the field, this is the ultimate reference for R in Network Analysis.

Author : Christopher J. Cramer
Publisher : John Wiley & Sons
Page : 624 pages
File Size : 40,9 Mb
Release : 2013-04-29
Category : Science
ISBN : 9781118712276

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Essentials of Computational Chemistry by Christopher J. Cramer Pdf

Essentials of Computational Chemistry provides a balanced introduction to this dynamic subject. Suitable for both experimentalists and theorists, a wide range of samples and applications are included drawn from all key areas. The book carefully leads the reader thorough the necessary equations providing information explanations and reasoning where necessary and firmly placing each equation in context.