BOOK REVIEWS
J. Chem. Inf. Comput. Sci., Vol. 37, No. 2, 1997 415
BOOK REVIEWS Classical and Three-Dimensional QSAR in Agrochemistry. Edited by Corwin Hansch and Toshio Fujita. ACS Symposium Series 606. American Chemical Society: Washington. 1995. x + 342 pp. $88.95. ISBN 0-8412-3321-7. This volume was developed from a symposium sponsored by the Division of Agrochemicals at the 208th National Meeting of the American Chemical Society in the fall of 1994. This reviewer attended most of the presentations at that symposium and was impressed at the time with the breadth of subjects and the caliber of the presentations. This volume generally preserves the high standards set at the meeting. The volume consists of 24 chapters, of which two are introductions by the editors. The remainder are divided into four sections, titled “Partitioning,” “Transport and Environmental Toxicology,” “Traditional QSAR and Molecular Modeling,” and “Newer Computational-Based Methods”. A few chapters are overviews of some aspect of QSAR in agrochemistry, but most are descriptions of emerging techniques, many of which were developed by the authors of the respective chapters. Particularly noteworthy are Fujita’s reports on bioisosteric transformations and on a new hydrophobicity parameter applicable to oligopeptides, the explanation of scaled rank-sum statistics by R. D. Clark et al., Y. C. Martin’s presentation of a method for addressing the alignment problem in CoMFA, and the demonstration by I. Moriguchi et al. of the use of fuzzy adaptive least-squares to noncongeneric QSAR. Other readers may have a different list of favorites, but there is abundant material to choose from. Many of the methods rely on quantum mechanical calculations, which have historically been the province of mainframes, but these calculations will become accessible to many more researchers as desktop computers continue to become more powerful. It is perhaps a sign of changing times that no paper even mentions chemical graph theory. As in nearly all symposium volumes, quality varies from one author to the next, but in this volume the good easily outnumber the bad. This reviewer found it particularly impressive that, in almost every case, techniques are presented with worked-out examples and in sufficient detail that a reader could not only follow the examples but also actually try out a technique in his or her own research. Thus, workers active in QSAR will find not only a summary of the state of the art but also many ideas for new approaches to their own data and interests. The volume might serve as an excellent starting point for anyone interested in learning and trying new methods in QSAR. At over $0.25 per page, the price seems a little high, but it is probably not out of line with today’s specialty scientific book market. This review was written by Gordon Cash in his private capacity. No official support or endorsement by the Environmental Protection Agency is intended or should be inferred.
Gordon G. Cash United States EnVironmental Protection Agency CI9604293 S0095-2338(96)00429-5
World Databases in Chemistry. Edited by C. J. Armstrong. World Databases Series. Bowker Saur: NJ. 1996. 1200 pages. $235.00. ISBN 1-85739-101-2. World Databases in Chemistry is the eighth in the World Databases Series. The overall aim of this series is to list all the databases (worldwide) available in various formats, in 23 broad subject categories. To that end, this directory defines Chemistry in the broadest sense and includes disciplines such as Agrochemistry, Forensic Chemistry, Thermochemistry, Pharmacology, Materials Science, Chemical Engineering and Manufacturing. World Databases in Chemistry provides comprehensive, evaluative, and comparative information on all types of publicly accessible databases in Chemistry that are available worldwide in any language and in any electronic form.
The directory is divided into ten sections starting with broad sections such as Chemistry (databases that are relevant across the whole spectrum of Chemistry) and Chemistry general (databases that do not fit into any other category), and is followed by seven specific areassOrganic, Organometallic and Petrochemistry; Inorganic; Analytical; Toxicology, Pollution and Waste Treatment; Pharmaceuticals and Cosmetics; Surface and Materials Chemistry; Chemical Engineering and Manufacture; and Patents. In each section the entries are grouped by database families and arranged alphabetically by the database name. For each unique database or information source there is a master record which gives a detailed description of the database including content, availability, coverage, etc. and includes evaluative information. This is followed by a smaller entry for each version of the database (different vendors, medium, etc.). The smaller entries are arranged by the medium and then by the online host/CD-ROM producer. Wherever possible third party evaluations and references to reviews are included. There is a subject index and an index of file names or alternative database names. There is also a listing of all database producers with addresses, phone and fax numbers, and e-mail addresses (subject to availability) which is very useful. This book is an excellent compilation of data, painstakingly done, and arranged logically providing links to the appropriate master database. It includes all types of databases ranging from the usual Chemical Abstracts, full text journal databases, Registry of mass spectral data, and molecular modeling databases. The record for full text journals could be improved. The start year listed in the record corresponds to the start year of the journal in print rather than online, and the access information is not clear. Apart from that minor inconsistency, this Directory is a gold mine and is worth its price for the information that is available. However, in this rapidly changing information environment and era of tight budgets, the balance between cost and usage is a delicate one and unique to each Library or Information Center.
Jayashri Nagaraja Princeton UniVersity CI960435Z S0095-2338(96)00435-0
Computer-Aided Molecular Design. Theory and Practice. By Jean-Pierre Doucet and Jacques Weber. Academic Press: San Diego. 1996. 457 pp. ISBN 0-12-221285-1. $89.95. There has long been a need for an advanced undergraduate or graduate textbook in computer-aided molecular design. Although many monographs and symposia have been published in this area, none of them have successfully drawn the subject together in a way suitable for teaching as well as this book. Tim Clark’s Computational Chemistry was the first to combine the various computational techniques together in a text, but his book is more focused on structure calculation techniques and is now somewhat dated. The book’s goal is to train undergraduates in the computer tools available to chemists. Despite the broad nature of computer-aided molecular design it achieves this goal. The book has 13 chapters two of which cover the structure calculation methods: empirical, semiempirical, and ab initio calculations. It also discusses more advanced concepts such as simulations, conformational analysis techniques, similarity, and drug receptor analysis. The essentials of protein structure and modeling are also discussed. The initial chapters cover the mathematics of graphics programming and algorithms for surface rendering. These chapters would be most interesting to students wishing to develop graphics software and not as interesting to those only using the software. In the text’s broad and even coverage the only notable omission is of 3D QSAR techniques, which now form an important part of the practical use of modeling.
416 J. Chem. Inf. Comput. Sci., Vol. 37, No. 2, 1997 The book could also be enhanced, for students and instructors, with exercises at the conclusion of each chapter. The book is successful at mixing theory and applications and at presenting the strengths and weaknesses of each. This is an important work and should be an important part of an advanced undergraduate or graduate level course in computational chemistry techniques. It is also an excellent reference work for workers in the field.
Matthew Clark Institute for Scientific Information CI960433E S0095-2338(96)00433-7
Computational Chemistry Using the PC. By Donald W. Rogers. VCH: New York. 1994. 247 pp. $65.00. ISBN 1-56081-672-4. Computational chemistry can be performed on a PC. With such an ambitious title, this book promises more than it delivers. The author sent this reviewer corrections in the mail. Some of the exercises had been published before, in American Laboratory, as mentioned in the foreword to the book. The first chapter concerns physical chemistry calculations and exercises. The answers to the exercises were most helpful in understanding the role of the PC in computing desired output values from estimated input values. Manual submission of new estimated values for several iterations of calculations was recommended by the author so that the correct value could be approached. Later exercises followed the same pattern. How to translate equations into computer language was not part of the text. The resulting example equations appeared in the accompanying calculation source code files and on disk. The author continued to use examples from physical chemistry in later chapters and did not branch out into areas involving chemical formulas, molecular weights, chemical composition, chemical structure, graph theory, molecular modeling, or quantum mechanics, all of which can be performed on a PC.
Charles E. Gragg Inter Nuts & Bolts, Inc. CI960436R S0095-2338(96)00436-2
Molecular Modeling from Virtual Tools to Real Problems. Edited by Thomas F. Kumosinski and Michael N. Liebman. ACS Symposium Series 576, American Chemical Society: Washington, DC. 1994. 516 pp with bibliographical references and index. $119.95. ISBN 0-8412-3042-0. Molecular Modeling is one of the ACS Symposium Seriessand as in the case of other similar monographssdeveloped from a symposium sponsored by the Division of Agricultural and Food Chemistry at the 205th National Meeting of the American Chemical Society, Denver, CO, March 28-April 2, 1993. A group of internationally recognized experts have organized this work in order to address the subject of “molecular modeling from
BOOK REVIEWS experiment to computation”. The growing interest in structure-function relationships in proteins has stimulated scientists to design useful experiments to study the functionality and then develop experimental and theoretical models to relate to structure. A variety of techniques are employed to determine protein structure at the secondary and tertiary levels. X-ray crystallography can provide detailed structure, but many proteins cannot be crystallized to a high degree of optical purity, and even when possible, the methodology is expensive in terms of time and cost. Reliable determination of the secondary structure can be obtained by applying less demanding methods such as circular dichroism (CD) and Fourier-transform infrared (FTIR) spectroscopy. The structural information, thus determined, can be further refined by molecular dynamics techniques. This book has been organized into three broad sections. The first section on “Molecular Structure: Experimental” contains chapters 2-10, in which the contributors have set the standards for designing and conducting appropriate experiments to obtain structural information. Emphasis has been placed on CD and FTIR techniques. Thomas Kumosinski and co-workers have presented an impressive panorama of work carried out at the Eastern Regional Research Center, U.S. Department of Agriculture, Philadelphia, PA. Chapter 6 titled “GlobalSecondary-Structure Analysis of Proteins in Solution” is very wellwritten and provides a systematic and sound approach to the determination of secondary structure using FTIR. The method of analysis based on fitting both amide I and II envelopes by nonlinear regression is rigorous and yet very practical in use. The validity and reliability of the method and analysis have been convincingly established. The second section titled “Molecular Structure: Analysis” includes chapters 11-21 on subjects, such as, implications of single amino acid substitution, comparison of spiral structures in wheat proteins, and modeling of biological pathways. Chapter 12 focuses on theoretical structure-function analysis of amino acid substitution in proteins. The effects of such computer “mutations” can be determined through a variety of computational techniques. Such techniques can provide molecular biologists with theoretical basis for undertaking point mutation projects in order to engineer protein molecules for specific purpose. The third section on “Molecular Interactions: Recognition” includes chapters 22-26 in which complex biological systems are studied through a combination of experimental and theoretical techniques. Chapter 23 is noteworthy in this regard as it deals with a fundamental question of protein-salt interactions that often result in changes in stability, structure, and state of aggregation of proteins in aqueous solutions. Molecular modeling techniques are highly useful in understanding such changes that have great importance in nature. Molecular Modeling is an authoritative compilation of foremost techniques used in studying structure-function relationships in proteins. The individual chapters are well-written, and the editors have done a superb job of presenting these together in a coherent manner. This work will become an essential reference for all those who are intrigued by the complexity of protein structure and aspire to engineer molecules for novel applications.
Narinder Singh UniVersity of Kansas Medical Center CI960438B S0095-2338(96)00438-6
