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Advanced Methods and Applications in Chemoinformatics: Research Progress and New Applications

Release Date: August, 2011. Copyright © 2012. 512 pages.
ISBN13: 9781609608606|ISBN10: 1609608607|EISBN13: 9781609608613|
DOI: 10.4018/978-1-60960-860-6
Cite Book

MLA

Castro, Eduardo A., and A. K. Haghi. "Advanced Methods and Applications in Chemoinformatics: Research Progress and New Applications." IGI Global, 2012. 1-512. Web. 28 Nov. 2014. doi:10.4018/978-1-60960-860-6

APA

Castro, E. A., & Haghi, A. K. (2012). Advanced Methods and Applications in Chemoinformatics: Research Progress and New Applications (pp. 1-512). Hershey, PA: IGI Global. doi:10.4018/978-1-60960-860-6

Chicago

Castro, Eduardo A., and A. K. Haghi. "Advanced Methods and Applications in Chemoinformatics: Research Progress and New Applications." 1-512 (2012), accessed November 28, 2014. doi:10.4018/978-1-60960-860-6

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Description

Chemoinformatics is a scientific area that endeavours to study and solve complex chemical problems using computational techniques and methods. The collection of topics in this book aims to reflect the diversity of recent advances in chemoinformatics with a broad perspective which may be useful for scientists as well as for graduate students and engineers. This book presents leading-edge research from around the world in this dynamic field.

Advanced Methods and Applications in Chemoinformatics: Research Methods and New Applications provides innovative chapters on the growth of educational, scientific, and industrial research activities among chemists and chemical engineers and provides a medium for mutual communication between international academia and the industry. This book contains significant research reporting new methodologies and important applications in the fields of chemical informatics as well as the latest coverage of chemical databases and the development of new computational methods and efficient algorithms for chemical software and chemical engineering.

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Table of Contents and List of Contributors

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Table of Contents
Preface
Eduardo A. Castro, A. K. Haghi
Chapter 1
Santanab Giri, Arindam Chakraborty, Ashutosh Kumar Gupta, Debesh Ranjan Roy, Ramadoss Vijayaraj, Ramakrishnan Parthasarathi, Venkatesan Subramanian, Pratim Chattaraj
In the present chapter, density functional theory based reactivity indices are applied as chemical descriptors in QSAR analysis for ecotoxicological... Sample PDF
Modeling Ecotoxicity as Applied to some Selected Aromatic Compounds: A Conceptual DFT Based Quantitative-Structure-Toxicity-Relationship (QSTR) Analysis
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Chapter 2
Francisco Torrens, Gloria Castellano
Algorithms for classification and taxonomy bases on criteria, e.g., information entropy. The feasibility of replacing a given molecule by similar... Sample PDF
Structural Classification of Complex Molecules by Artificial Intelligence Techniques
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Chapter 3
Bakhtiyor Rasulev, Danuta Leszczynska, Jerzy Leszczynski
Here, the authors show that an application of the QSAR methods for nanomaterials is nevertheless possible and can be useful in predicting their... Sample PDF
Nanoparticles: Towards Predicting Their Toxicity and Physico-Chemical Properties
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Chapter 4
Laurent A. Baumes
The data mining technology increasingly employed into new industrial processes, which require automatic analysis of data and related results in... Sample PDF
Active Learning and Mapping: A Survey and Conception of a New Stochastic Methodology for High Throughput Materials Discovery
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Chapter 5
Abdelmalek Amine, Zakaria Elberrichi, Michel Simonet, Ali Rahmouni
In order to identify new molecules susceptible to become medicines, the pharmaceutical research has more and more resort to new technologies to... Sample PDF
Molecular Similarity: Combining Neural Networks and Knn Methods
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Chapter 6
Lionello Pogliani
Valence molecular connectivity indices are indices based on the concept of valence delta, d v, that can be derived from general chemical graphs or... Sample PDF
A QSAR/QSPR Study with Graph-Theoretical Indices based on a New Type of Vertex Degree
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Chapter 7
Mihai V. Putz, Ana-Maria Putz
The logistic temporal solution of the generalized Michaelis-Menten kinetics is employed to provide a quantum basis for the tunneling time and energy... Sample PDF
Logistic vs. W-Lambert Information in Modeling Enzyme Kinetics at Quantum Level
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Chapter 8
Željko Debeljak, Marica Medic-Šaric
During the last few decades the number of available molecular descriptors has grown exponentially. A reduced set of descriptors, containing only... Sample PDF
Advances in Relevant Descriptor Selection
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Chapter 9
D. Shanthi, L. Rajendran
The system is considered here with two chemical species, the reactant a and autocatalyst b. The Gray-Scott model of cubic-autocatalysis with linear... Sample PDF
Analytical Solution of Cubic Autocatalytic Reaction-Diffusion Equations: Homotopy Pertuburation Approach
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Chapter 10
Pablo R. Duchowicz, Eduardo A. Castro
Present chapter reviews the application of Quantitative Structure-Activity Relationships for the treatment of molecules involving thousands of... Sample PDF
On Applications of Macromolecular QSAR Theory
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Chapter 11
Alan Talevi, Eduardo A. Castro, Luis E. Bruno-Blanch
In this chapter, the authors analyze virtual screening advantages and the classification of virtual screening approaches. They also discuss the... Sample PDF
Virtual Screening: An Emergent, Key Methodology for Drug Development in an Emergent Continent. A Bridge Towards Patentability.
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Chapter 12
Hamid Dadvar, Farhad E. Ghodsi, Saeed Dadvar
In this chapter, the sol-gel made titanium dioxide nanostructured thin films deposited on special substrates such as glasses, mica, steels... Sample PDF
Synthesis, Properties, and Applications of Special Substrates Coated by Titanium Dioxide Nanostructured Thin Films via Sol-Gel Process
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Chapter 13
Sonia Ilieva, Boris Galabov
Numerous applications showed that the EPN index, an accurate quantum mechanical quantity, predicts with remarkable accuracy the energy shifts... Sample PDF
Electrostatic Potential at Nuclei: An Accurate Reactivity Descriptor for Organic Compounds
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Chapter 14
Jordi Vallverdú
Computer sciences have deeply changed the way by which we make science or produce knowledge. With the era of computers and the development of... Sample PDF
An Epistemological Analysis of QSPR/QSAR Models
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Chapter 15
Kshatresh Dutta Dubey, Rajendra Prasad Ojha
Computational techniques are widely used in the chemoinformatics and bioinformatics. Most of the drugs produce their effect by interacting with the... Sample PDF
Computational Techniques in Binding Affinity Prediction of Drugs
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Chapter 16
J.M. Villalba, R. Varón, E. Arribas, R. Diaz-Sierra, F. Garcia-Sevilla, F. Garcia-Molina, M. Garcia-Moreno, M. J. Garcia-Meseguer
The symbolic time course equations corresponding to a general model of a linear compartmental system, closed or open, with or without traps and with... Sample PDF
Symbolic Equation for the Instantaneous Amount of Substance in Linear Compartmental Systems: Software Furnishing the Coefficients Involved in it
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Chapter 17
Kunal Roy, Rudra Narayan Das
Development of predictive models has been accepted as an important strategy to aid in toxicity screening of chemicals, determination of... Sample PDF
On Extended Topochemical Atom (ETA) Indices for QSPR Studies
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Reviews and Testimonials

The main objective of this book is to provide innovative chapters on the growth of educational, scientific, and industrial research activities among chemists and chemical engineers and provides a medium for mutual communication between international academia and the industry. Reporting new methodologies and important applications in the fields of chemical informatics as well as includes the latest coverage of chemical databases, this book aims to present leading-edge research from around the world in the dynamic field of chemoinformatics.

– Dr. Eduardo A. Castro, Research Institute of Theoretical and Applied Physical-Chemistry (INIFTA), Argentina; and Dr. A.K. Haghi, University of Guilan, Iran
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Topics Covered

  • Classification of Complex Molecules by Artificial Intelligence Techniques
  • CORAL: QSPR/QSAR for Organometallic Substances
  • Future Challenges in Nanotechnology
  • Genetic Algorithm Optimization
  • Modelling Enzyme Kinetics
  • Molecular Connectivity Indices
  • Molecular Electronic Structures
  • QSAR Inhibitors of HIV
  • Similarity Measures in Chemoinformatics and Drug Design
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Preface

Using computational techniques and methods, chemoinformatics aims to study and solve complex chemical problems. The collection of topics in this book aims to reflect the diversity of recent advances in chemoinformatics with a broad perspective which may be useful for scientists as well as for graduate students and engineers.

The main objective of this book is to provide innovative chapters on the growth of educational, scientific, and industrial research activities among chemists and chemical engineers and provides a medium for mutual communication between international academia and the industry.  Reporting new methodologies and important applications in the fields of chemical informatics as well as includes the latest coverage of chemical databases, this book aims to present leading-edge research from around the world in the dynamic field of chemoinformatics.

Advanced Methods and Applications in Chemoinformatics: Research Methods and New Applications is made up of 17 chapters which will provide insight on this very topic as a whole.

Chapter 1 introduces quantitative structure activity relationship (QSAR) as a mathematical representation of biological activity in terms of structural descriptors. The chapter will present density functional theory based reactivity indices are applied as chemical descriptors in QSAR analysis for ecotoxicological studies on a group of aromatic compounds.

Chapter 2 indicates that the feasibility of replacing a given molecule by similar ones in the composition of a complex drug is studied. In taxonomy the detailed comparison of the sequences of biomolecules, proteins or nucleic acids, allows the reconstruction of a molecular phylogenetic tree.

Chapter 3 explains that nanomaterials are becoming an important component of the modern life and have been the subject of increasing number of investigations involving various areas of natural sciences and technology. However, theoretical modeling of physicochemical and biological activity of these species is still very scarce.

Chapter 4 reviews the active learning methodology, and a new one that aims at generating successively new samples in order to reach an improved final estimation of the entire search space investigated according to the knowledge accumulated iteratively through samples selection and corresponding obtained results, is presented. The methodology is shown to be of great interest for applications such as high throughput material science and especially heterogeneous catalysis where the chemists do not have previous knowledge allowing to direct and to guide the exploration.

Chapter 5 studies molecular similarity using a particular type of neural networks: the Kohonen networks (also called “SOM” Self- Organizing Maps), applying the nearest neighbor algorithm to the projection of the molecules (coordinates) in the constructed MAP.

Chapter 6 is a QSAR/QSPR study with a graph-theoretical centered on a vertex degree based on simple, general (or pseudograph), and complete graphs has shown the ability of the, connectivity, pseudoconnectivity and dual indices to achieve a quite good model of activities (LogP) in six different media and of four properties of two different and highly heterogeneous classes of compounds.

Chapter 7 explains that the logistic temporal solution of the generalized Michaelis-Menten kinetics is employed to provide a quantum basis for the tunnelling time and energy evaluations of Brownian enzymic reactions. The mono-substrate and mixed inhibition cases are treated and the associated quantum diagrams of the reaction mechanisms are depicted in terms of intermediate enzyme complexes.

Chapter 8 provides an Overview of the most important feature selection methods, their advantages, disadvantages and applications in SAR and QSAR is given.

Chapter 9 presents the approximate analytical and numerical solution of cubic autocatalytic reaction-diffusion equations. There is a great deal of interest in chemical reactions which exhibit oscillatory solutions. These oscillations occur due to feedback in the system either chemical feedback such as autocatalysis or temperature feedback due to non-isothermal reaction.

Chapter 10 reviews the application of Quantitative Structure-Activity Relationships for the treatment of molecules involving thousands of atoms, such as proteins, nucleic acids (DNA, RNA), or polysaccharides. This is a new developing area of interest in Chemoinformatics, and it is expected to have a growing number of applications during the forthcoming years. Among the several points to be addressed during the modeling of macromolecules, the most important one appears to be the accurate representation of the chemical structure through numerical descriptors. It has to be noticed that descriptors based on optimized three-dimensional geometry are difficult to specify, and it is also a drawback the fact that the experimental geometry is not available.

Chapter 11 analyzes virtual screening advantages and the classification of virtual screening approaches.  Also discussed is the current and potential importance of virtual screening for drug development in Latin America. Finally, the authors present a brief overview on virtual screening perspectives.

Chapter 12 generalizes the sol-gel made titanium dioxide nanostructure thin films deposited on special substrates such as glasses, mica, steels, textiles, fibers, and other organic/inorganic substrates were reviewed. Through this review, several distinctive properties such as optical, electrical, photocatalytic, morphological, and mechanical properties of TiO2 nanostructured thin films were described.

Chapter 13 surveys the application of the electrostatic potential at nuclei (EPN) as a reactivity index in quantifying hydrogen bonding as well as different reactions of organic compounds. Numerous applications showed that the EPN index, an accurate quantum mechanical quantity, predicts with remarkable accuracy the energy shifts accompanying hydrogen bonding.

Chapter 14 explains the era of computers and the development of computer science, quantum chemists were among the first scientists to explore the potentialities of the new tool, and even to collaborate in its development. In this way, they also became participants in what many dubbed as the Second Instrumental Revolution in chemistry.

Chapter 15 discusses some of the most common techniques which are widely used in bioinformatics and chemoinformatics. Most of the drugs produce their effect by interacting with the target molecules via different interactions. However, these interactions are tough to be calculated without use of robotics techniques.

Chapter 16 presents the symbolic time course equations corresponding to a general model of a linear compartmental system, closed or open, with or without traps and with zero input. Special attention is given to the open systems, for which an exhaustive kinetic analysis has been developed to obtain important properties.

Chapter 17 focuses on extended topochemical atom (ETA) indices, a relatively new class of topological descriptors. ETA indices contain important information regarding the nature of the atoms, bonds, atomic electronic environment and consider the contribution of different functional groups, molecular fragments, and branching to the response as evidenced by different reports showing their successful application in modeling different endpoints including toxicity, drug activity, and physicochemical properties.

With this collection, this book will provide innovative chapters on the growth of educational, scientific, and industrial research activities among chemists and chemical engineers and provides a medium for mutual communication between international academia and the industry.
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Author(s)/Editor(s) Biography

Eduardo A. Castro’s career was launched by studying Physical Chemistry at the Faculty of Chemistry of the La Plata National University of La Plata, Buenos Aires, Argentina, during 1963-70. His diploma work to get his PhD Degree was on calculation of HMO and related semi empirical methods of beta-carotene for analyze chemical reactivity and electronic spectrum. Incidentally, his only available computational resource on that time was a diagonalization subroutine for symmetric matrices and his only disposable instruction book was Andrew Streitwieser´s on Theoretical Organic Chemistry. From 1971-72 he performed his Ph.D. work at the Physics Department of the National La Plata University, working under supervision of Manuel Sorarrain. After that we find him as a research scientist at the Theoretical and Applied Research Institute located at La Plata National University where he founded the Group for Theoretical Chemistry in 1974. Then, he was appointed as a member of the Scientific Researcher Career in the Argentina National Research Council, and he continues up to the present time as a Superior Researcher.
A. K. Haghi holds a BSc in urban and environmental engineering from the University of North Carolina (USA); a MSc in mechanical engineering from North Carolina A&T State University (USA); a DEA in applied mechanics, acoustics and materials from Université de Technologie de Compiègne (France); and a PhD in engineering sciences from Université de Franche-Comté (France). He is the author and editor of 165 books as well as 1000 published papers in various journals and conference proceedings. Dr. Haghi has received several grants, consulted for a number of major corporations, and is a frequent speaker to national and international audiences. Since 1983, he served as a professor at several universities. He is currently Editor-in-Chief of Polymers Research Journal and on the editorial boards of many international journals. He is also a faculty member of University of Guilan (Iran) and a member of the Canadian Research and Development Center of Sciences and Cultures (CRDCSC), Montreal, Canada.
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Editorial Board

  • P. D. Ariel, Trinity Western University, Canada
  • M. Ciocoiu, Technical University of Asachi, Romania
  • G. Denuault, University of Southampton, UK
  • A. Hamrang, Industrial Engineer, UK
  • Ji-Huan He, Donghua University, China
  • V. Mottaghitalab, University of Guilan, Iran
  • F. Naghiyev, Azerbaijan State Oil Academy, Azerbaijan
  • S. Thomas, Mahatma Gandhi University, India
  • H. Ghanadzadeh, University of Guilan, Iran
  • J. Kamm, University of Toledo, USA
  • L.A.Pothan, Bisop Moore College, India
  • G.E. Zaikov, Russian Academy of Sciences, Russia