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Protein structure prediction:
Biochemistry and Molecular Biology Education 29 (2001) 33}38
Book reviews Protein structure prediction: Methods and protocols D.M. Webster (Ed.); Vol. 143, Methods in Molecular Biology J.M. Walker, Series Editor); Humana Press, Totowa, NJ, 2000, ISBN 0-089603-637-5 Experimental techniques for the determination of three-dimensional (3D) macromolecular structures can often involve months or even years of e!ort. As a result, the number of 3D structures available in the central repository for this information: the Protein Data Bank (http://www.rcsb.org/pdb/), is a tiny fraction of the number of sequences known. With the huge amount of sequence data that constantly #ows out of various genomic sequencing projects, this gap will continue to widen. The ultimate goal of structure prediction is to be able to feed a sequence into a computer and immediately generate a 3D structure, however, understanding the way that proteins fold remains one of the major challenges in biology. Attacking the structure prediction problem from a number of angles simultaneously is leading to many advances, and this book provides a timely review of the current methodologies. The book is a collection of 18 review articles, many written by distinguished experts in their "eld, providing an overview of the major aspects of protein structure prediction. About half of the articles deal with speci"c software packages, many of which are free to academic users, where the author of the article is often the author of the software discussed. This has the disadvantage of lacking a critical comparison of techniques, but is more than made up by the many useful hints and tips authors give on how to use their software. These comments add to the more informal nature of the articles compared with standard review papers, making them accessible to the novice. Currently one of the most useful techniques in structure prediction, is when the sequence of unknown structure is similar to one with a known structure. This is not as unlikely as may be expected, since the number of possible ways that proteins fold appears to be relatively small (probably less than 2000). Unfortunately, detecting such similarities is a major obstacle. Predicting a structure in this way involves sequence and structure analysis, as well as the practicalities of modelling a sequence onto a structural template. All of these are covered in detail by the book. However, it does not limit itself to these, but also covers less well-established topics as diverse as modelling transmembrane helices, ab initio techniques, and protein docking.
Advances in the "eld of structure prediction are assessed by an ongoing biannual competition of &blind' prediction, the Critical Assessment of techniques for protein Structure Prediction (CASP; http://predictioncenter.llnl.gov/). Researchers from around the world can access a list of sequences whose structures are soon to be determined; then predicted structures are compared with the experimental results by a panel of experts. The online results from CASP provide the most up-to-date assessment of the state of the art with regard to prediction techniques. Two main aspects detract from the overall quality of the book. The "rst is that the inevitable delay in bringing such a book to publication means that many of the authors refer to CASP2 (from 1996), whereas CASP4 took place in December 2000, also a number of URLs cited are no longer accessible. The former point is less serious since much of the progress made in the intervening time is mainly due to improvements in the underlying computation, whereas the software interface to a novel user may remain largely unchanged. The other irritation relates to the editing. There are a number of small typographical errors, for example in URLs, and transposed labels of graphs and tables. Despite these, it is certainly a useful reference to address for anyone thinking of dipping their toes into this exciting "eld. Kurt Giles Department of Experimental Psychology, Oxford University, Oxford OX13UD, UK PII: S 1 4 7 0 - 8 1 7 5 ( 0 0 ) 0 0 0 6 3 - 1
Fundamentals of enzymology (Third Edition) Nicolas C. Price, Lewis Stevens; Oxford University Press, Oxford, 1999 The book Fundamentals of Enzymology, true to its title, is an overview of enzymology that can be used in a survey course on the subject. The paperback book is 449 pages in length, and the book includes in addition a 19-page appendix listing the common and Enzyme Commission names and numbers of the enzymes mentioned in the text, as well as an 8-page index. The book is organized into a brief introductory chapter followed by chapters on puri"cation of enzymes, structure of enzymes, introduction to enzyme kinetics, mechanism of enzyme action, control of enzyme activity, enzymes in
Book reviews Protein structure prediction: Methods and protocols D.M. Webster (Ed.); Vol. 143, Methods in Molecular Biology J.M. Walker, Series Editor); Humana Press, Totowa, NJ, 2000, ISBN 0-089603-637-5 Experimental techniques for the determination of three-dimensional (3D) macromolecular structures can often involve months or even years of e!ort. As a result, the number of 3D structures available in the central repository for this information: the Protein Data Bank (http://www.rcsb.org/pdb/), is a tiny fraction of the number of sequences known. With the huge amount of sequence data that constantly #ows out of various genomic sequencing projects, this gap will continue to widen. The ultimate goal of structure prediction is to be able to feed a sequence into a computer and immediately generate a 3D structure, however, understanding the way that proteins fold remains one of the major challenges in biology. Attacking the structure prediction problem from a number of angles simultaneously is leading to many advances, and this book provides a timely review of the current methodologies. The book is a collection of 18 review articles, many written by distinguished experts in their "eld, providing an overview of the major aspects of protein structure prediction. About half of the articles deal with speci"c software packages, many of which are free to academic users, where the author of the article is often the author of the software discussed. This has the disadvantage of lacking a critical comparison of techniques, but is more than made up by the many useful hints and tips authors give on how to use their software. These comments add to the more informal nature of the articles compared with standard review papers, making them accessible to the novice. Currently one of the most useful techniques in structure prediction, is when the sequence of unknown structure is similar to one with a known structure. This is not as unlikely as may be expected, since the number of possible ways that proteins fold appears to be relatively small (probably less than 2000). Unfortunately, detecting such similarities is a major obstacle. Predicting a structure in this way involves sequence and structure analysis, as well as the practicalities of modelling a sequence onto a structural template. All of these are covered in detail by the book. However, it does not limit itself to these, but also covers less well-established topics as diverse as modelling transmembrane helices, ab initio techniques, and protein docking.
Advances in the "eld of structure prediction are assessed by an ongoing biannual competition of &blind' prediction, the Critical Assessment of techniques for protein Structure Prediction (CASP; http://predictioncenter.llnl.gov/). Researchers from around the world can access a list of sequences whose structures are soon to be determined; then predicted structures are compared with the experimental results by a panel of experts. The online results from CASP provide the most up-to-date assessment of the state of the art with regard to prediction techniques. Two main aspects detract from the overall quality of the book. The "rst is that the inevitable delay in bringing such a book to publication means that many of the authors refer to CASP2 (from 1996), whereas CASP4 took place in December 2000, also a number of URLs cited are no longer accessible. The former point is less serious since much of the progress made in the intervening time is mainly due to improvements in the underlying computation, whereas the software interface to a novel user may remain largely unchanged. The other irritation relates to the editing. There are a number of small typographical errors, for example in URLs, and transposed labels of graphs and tables. Despite these, it is certainly a useful reference to address for anyone thinking of dipping their toes into this exciting "eld. Kurt Giles Department of Experimental Psychology, Oxford University, Oxford OX13UD, UK PII: S 1 4 7 0 - 8 1 7 5 ( 0 0 ) 0 0 0 6 3 - 1
Fundamentals of enzymology (Third Edition) Nicolas C. Price, Lewis Stevens; Oxford University Press, Oxford, 1999 The book Fundamentals of Enzymology, true to its title, is an overview of enzymology that can be used in a survey course on the subject. The paperback book is 449 pages in length, and the book includes in addition a 19-page appendix listing the common and Enzyme Commission names and numbers of the enzymes mentioned in the text, as well as an 8-page index. The book is organized into a brief introductory chapter followed by chapters on puri"cation of enzymes, structure of enzymes, introduction to enzyme kinetics, mechanism of enzyme action, control of enzyme activity, enzymes in