Essential Cell Biology, Second Edition contains basic, core knowledge about how cells work. It has a proven track record in providing students with a conceptual and accessible grounding in cell biology. The text and figures have been prepared to be easy-to-follow, accurate, clear and engaging for the introductory student. Each section follows logically from the previous one, telling a story, rather than being a collection of facts. Questions integrated throughout each chapter encourage the reader to pause, think about what they have read, and attempt to apply the new knowledge in ways that test their understanding. Based on user feedback, the Second Edition now offers increased coverage of genetics and more experimental background. It is completely up-to-date.
"an essential reference for practicing plant biologists and for the increasing number of scientists from other disciplines who are entering the field of plant biology. To exploit fully the wealth of new information provided by the genome projects and to integrate the metabolic, regulatory, and signal transduction pathways of complex organisms, biologists will require a solid command of biochemistry and physiology. For this reason, the publication of
Biochemistry Molecular Biology of Plants could not have come at a more opportune and auspicious time."
This book is meticulously organised and richly illustrated, useful both for teaching and for reference. The multi-authored work provides a contemporary view of its subject, including molecular biology, cell biology, and plant physiology, integrated around the themes of:
"The great strength of this book is that it has integrated its three major components (molecular biology, cell biology, and plant biochemistry) in each of the 24 chapters, resulting in a comprehensive analysis of a multitude of specific topics."
Researchers in the pharmaceutical, biotechnology, and agribusiness industries
A CD-ROM of all illustrative matter in the book is available separately.
Customer Reviews:
love it.......2006-11-10
This book has the basis of Molecular and cell Biology that make you well armed. It has great pictures too. The biochemistry also is awesome, you'll find all the pathways you want. I even not gonna sell it after i graduate. I prefer keep it.
Best Plant Biol. book out there.......2005-11-17
I am a PhD candidate in Plant Sciences and I work with both applied and basic researchers who work on all aspects of plant biology/agriculture etc. Everyone I work with and myself included feel that this is the best single plant biology text. It is a few years old now so some of the mol. biology will be outdated, and a couple of examples have since been proven to be different than described in the book, but this is minor. This is for the adv. undergrad or graduate student and if you are a graduate student in plant biology you should have this book-it is very expensive, but nearly every post-doc/grad student I know has a copy. Get the hardcover it will hold up better.
Biochemistry & Molecular Biology of Plants.......2004-03-26
Mr. !!!
>
> I am Brazilian and I am student of Post-Graduate in Agronomy, no conditions. I do like the books:
Biochemistry & Molecular Biology of Plants
Author: Robert Buchanan, Wilhelm Gruissem, Russell L. Jones
(Paperback)
Usually ships in 1-2 weeks
Our Price: $124.95
However, I do not have acquire in the BRAZIL. Thus, I would like to know if you could help me, sending for me this books.
I thank your attention and I wait to be able to count on the your
contribution.
Yours truly,
Roberto Cunha
Street Address = Rua Dr. Milton Bandeira nº 34 ap 306
City- Viçosa
Province/State - MINAS GERAIS
Postal Code/Zip Code - 36570000
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Evening Telephone Number - 0 31 31 38923607
Explanations not very comprehensive.......2003-07-15
The text covers a wide variety of plant molecular biology which is convienent. However the explanations are often very vague and do not connect with each other. When reading a paragraph you are often left with unanswered questions and the next paragraph may not connect with the previous paragraph at all. Not at all recommended for the beginner or undergraduate.
Comprehensive.......2001-10-12
This text book is astoundingly comprehensive. It covers all aspects of plant biochemistry and is written for the advanced undergraduate or graduate student. Great resource as reference material.
Average customer rating:
- A good introduction to the topic
- Well written, short explanations but nevertheless understandable
|
Microarray Gene Expression Data Analysis: A Beginner's Guide
Helen Causton ,
John Quackenbush , and
Alvis Brazma
Manufacturer: Blackwell Publishing Limited
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Data Analysis Tools for DNA Microarrays
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Bioinformatics For Dummies (For Dummies (Math & Science))
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Guide to Analysis of DNA Microarray Data, Second Edition
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The Analysis of Gene Expression Data
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Statistical Analysis of Gene Expression Microarray Data
ASIN: 1405106824 |
Book Description
Microarray technology is arguably the most important recent breakthrough in molecular biology. It enables researchers to obtain snapshots of gene expression for all the genes in a genome in a single experiment. Microarray experiments generate massive amounts of data that can be analysed to extract new knowledge about the underlying biological processes.This guide covers aspects of designing microarray experiments and analysing the data generated, and includes information on some of the tools that are available from non-commercial sources. Concepts and principles underpinning gene expression analysis are emphasised, and wherever possible the mathematics has been simplified. The guide is intended for use by graduates and researchers in bioinformatics and the life sciences and is also suitable for statisticians who are interested in the approaches currently used to study gene expression.
Customer Reviews:
A good introduction to the topic .......2007-05-20
Microarrays are a tool for monitoring gene expression levels for thousands of genes in parallel. This technology is very useful since patterns in the gene expression can be used for molecular characterization of phenomena that range from disease states and response to stimuli to the differences between cells of different types. The amount of information obtained from one microarray experiment can be large. These large amounts of information present new challenges in the areas of data storage, management, and analysis by biologists who are not accustomed to dealing with this much data. Also, the software used for data analysis is usually written by mathematicians and statisticians that have a minimum of training in biology.
This book addresses some of the issues faced by researchers who are beginning their first microarray experiments. It covers various aspects of designing and analyzing the results of microarray experiments. Microarrays are not limited to the study of gene expression, but this remains the most common use of the technology and therefore is the only use of arrays discussed here. This book attempts to explain the underlying concepts and principles routinely used in analysis of gene expression data. The book should be accessible by statisticians, computer scientists, and students of bioinformatics who want a grounding in the types of analysis currently used to study microarray data.
The book begins with an introductory chapter which is followed by three major chapters. As with any technology that has the capacity to detect small changes in a highly dynamic system, the underlying experimental design and the manner in which an experiment is conducted is critical for obtaining high quality data. Chapter two addresses these issues. The raw data from microarray experiments are images that must be transformed and organized into gene expression matrices. These transformations are the subject of chapter 3. Finally, in chapter 4, the common methods used for analyzing gene expression data matrices with the goal of obtaining new insights into biology are discussed. The book does a pretty good job of providing the reader with a general understanding of the nature of microarray data and how it can be analyzed. It was never meant to be a reference book or a comprehensive review, just a gentle introduction.
Well written, short explanations but nevertheless understandable.......2005-07-06
Certainly, this book can not give a complete description of microarrays, neither from an experimental nor a theoretical side. Nevertheless, the issues presented and discussed provide the reader with a solid basis for more advanced studies.
In my opinion, this book is well written, the explanations given are descriptive and understandable and its overall organization is plausible. I recommend this book as an introduction for the analysis of microarray data, because it provides a good overview of existing methods in this field. A warning: This does not mean, that all these methods are thorougly expained! It just provides an overview!! If you want to learn, e.g., clustering methods, you should consult another book (probably no other book about microarrays but a decent book dealing only with data analysis in general or clustering methods...)
Amazon.com
Michael J. Behe, a biochemist at Lehigh University, presents here a scientific argument for the existence of God. Examining the evolutionary theory of the origins of life, he can go part of the way with Darwin--he accepts the idea that species have been differentiated by the mechanism of natural selection from a common ancestor. But he thinks that the essential randomness of this process can explain evolutionary development only at the macro level, not at the micro level of his expertise. Within the biochemistry of living cells, he argues, life is "irreducibly complex." This is the last black box to be opened, the end of the road for science. Faced with complexity at this level, Behe suggests that it can only be the product of "intelligent design."
Book Description
The groundbreaking, "seminal work" (Time) on intelligent design that dares to ask, was Darwin wrong?
In 1996, Darwin's Black Box helped to launch the intelligent design movement: the argument that nature exhibits evidence of design, beyond Darwinian randomness. It sparked a national debate on evolution, which continues to intensify across the country. From one end of the spectrum to the other, Darwin's Black Box has established itself as the key intelligent design text -- the one argument that must be addressed in order to determine whether Darwinian evolution is sufficient to explain life as we know it.
In a major new Afterword for this edition, Behe explains that the complexity discovered by microbiologists has dramatically increased since the book was first published. That complexity is a continuing challenge to Darwinism, and evolutionists have had no success at explaining it. Darwin's Black Box is more important today than ever.
Download Description
From within the highest ranks of the scientific community comes a startling new theory of creation that not only contradicts Darwinian orthodoxy but opens the door to theological arguments biologists have dismissed and ridiculed for more than a century.
Customer Reviews:
A Design Parade.......2007-10-08
After I purchased biochemist Michael Behe's new book "The Edge of Evolution," I decided it would be wise for me to boney up on his seminal 1996 work "Darwin's Black Box." I already played muck-a-muck with this debate for quite a few months, in a whirling attempt of absorbed concentration in the infamous struggle of "Design v. Darwin" to find out the truth. The debate may be superfluous, and especially downright nasty, and it will continue to intensify in the coming months with a new documentary by lawyer and social commentator Ben Stein in February 2008. Reading Behe is like taking a time out from the unfair play on both sides of the field. He is a better penman than Richard Dawkins, devoid of the man's vile poison, and he treats the reader as a student to be respected, not as a clay figure to be molded into a Darwiniac inquisitor. In fact, Behe is a committed believer in common descent, a position that isn't too friendly a bedfellow of creationists. The book is unique in both its author and its content, as demonstrated by the numerous "critiques" and "debunking" of the arguments proposed on the Amazon boards. Reading the hundreds or so reviews and responses only do so much to strengthen Behe's ideas.
This book is more like a parade. Behe, the ringleader with the marching rod, introduces us to the central argument of the "Black Box." It turns out to be irreducible complexity, which embodies the fabric of many biological systems once believed to be inconsequential, simplistic globules developed by chance mutation and selection. We then witness the march of the band and its many sections: the cell, the bacterial flagellum, blood-clotting, the cilium, etc. Each system, composed of many interdependent parts, will cease functioning if only one of its microscopic parts is missing. The individual parts, of course, can still possibly perform some other function (so goes the most powerful critique against ID! Things have different functions! Eureka!). However, the system itself will be quite useless. Thus appears the grand finale, a prolonged beat of the bass drum, which is that the neo-Darwinian paradigm is an implausible explanation for how these molecular systems appeared, no matter how many billions of years you attempt to postulate for its progress.
Attacking the hypothesis of intelligent design as a "God-of-the-Gaps" argument is one of the most frequently peddled mischaracterizations in all of the debate, promoted by no less than the most rabid of atheistic biologists like Dawkins and Eugenie Scott. The argument goes: We cannot envision a way naturalistic science could develop this system; hence it was made by God. The falsehood in this attack is typical, not to mention simplistic. Behe himself describes ID as the purposeful arrangement of parts in a system. We see this in every biological system: the cell, the flagellum, the cilium, and the blood clotting system. These systems are arranged in a purposeful pattern, structured precisely to, in the case of the cell, to replicate and store information, and in the case of other biological organisms, to sustain itself (unlike non-living materials like, say, rocks). It says nothing about whom or what this designer is. And, of course, it still remains the burden of proof to demonstrate how it evolved. We're talking about the Supreme Law of the Universe (Darwinism), and all that people can come up with are fairy tales about how it MIGHT have happened?
Neo-Darwinism cannot be supported much longer. It doesn't mean that evolution did not occur, or that common descent is a bogus idea. But the chance mutation-selection paradigm is becoming increasingly to difficult to sustain. The hyperactive Stalinist response to events like the Dover case and the actions committed by groups like the NSTA and ASE in America suggests a religious cult going through panic mode. Certainly there is something to what Behe and the rest of the ID movement is saying that just strikes a nerve. Maybe it's just the truth.
A great critique of evolution........2007-09-25
Supporters of the classic evolution that is taught in schools went nuts when this book was published. It could be argued that Michael Behe started the inteligent design theory and brought the debate of evolution back public stage.
Behe has been heavily criticized for daring to confront the evolution juggernaught and has made his book a must read for anyone interested in the evolution debate. This book is important and will shape the thinking of evolutionary scientists in the future, whether they like it or not.
Behe's empty box.......2007-09-05
First let's start with a quote from The National Academy of Science. " Creationism, I.D. and other claims of supernatural intervention in the origin of life of species are not science because they are not testable by the methods of science."
Mr. Behe uses the terms darwinism, darwinian evolution, darwinian gradualism through-out his book instead of modern evolution because he knows this name carries alot of heated imagery in the minds of the fundamentalist. If confronted with the findings of modern day evolution I think Mr. Behe would realize just how shakey the ground for his ideas would become.
He condems Prof. Doolittle for using a "yin yang" analogy but goes on to give boring and irrealivant analogy after analogy of his own.
He states that 90 persent of Americans believe in God as if the truth were dictated by a show of hands. If that were true then he might want to convert to Islam since the Muslim faith is the largest religious group in the world.
This leads me to my next problem with Mr. Behe's book. He is constantly refering to an intelligent designer or intelligent agent, and then speaking of the supernatural and divine. Here I have two questions.
1. Why use the singular noun? Why not appeal to many intelligent designers or agents?
2. Why could'nt these creators be "natural" as opposed to supernatural?
Which leads me to my final gripe.
Mr. Behe is constantly telling us how the scientific evidence points to an intelligent designer but never offers his own testable proof. Complexity is not proof in and of itself. What is the indentity of this creator? He does'nt say. The whole book seemed to be a rant against scientist who do not agree with his view. Mr. Behe seems to think there's this big conspiracy against the truth. Who's truth? His.
Amazing stuff.......2007-08-31
Functionally interdependent irreducible complexities....fascinating. How can these be adequately explained? I find it truly amazing.
Wonderful.......2007-08-22
Down to earth with complexity explained in a simple readable way. This is a very good source to dispute one of the most absurd notions in the history of the world....evolution. Fantastic, logical, and full of expert knowledge. Dispute it if you wish, but truth is evident. God is real!
Book Description
Molecular Biology, 3/e emphasizes the experimental data and results that support the concepts of molecular biology: DNA transcription, translation, replication, and repair. Experimental methods are extensively covered. The text presumes a prior course in general genetics.
Customer Reviews:
Molecular Biology.......2007-09-18
The book has been extremely useful for my Molecular Biology class as it completely integrates general and specific information about theory and practice in order for one to understand the basic ideas and reinforce with practical examples and not to mention very helpful diagrams. Great investment.
Molecular Biology by Robert F. Weaver .......2007-05-14
Best overview yet. Text particulary useful to follow logical flow of information. Very useful content. Well written.
fabulous.......2006-03-11
the item is in excellent condition.The service is so good that I am gonna shop from amazon, everytime I need a book.
Great text for those seeking to become a scientist........2005-11-06
The negative aspects that many reviewers seem to leverage against this book are the same aspects I find most useful and that make this text standout. This is an excellent text, written to help develop not merely an understanding of the subject material, but more broadly, to understand how to approach things like a scientist. I bought this book for a Euk MolBio undergraduate course which was taught roughly half from this book, and half from primary literature, and found the approach excellent in helping to improve the accessibility of any scientific paper, in addition to improving my own experimental design abilities. There are many useful diagrams presented, and a plethora of primary experimental findings that form the backbone of our current knowledge base. This book highlights the seminal experiments and thought processes that molded the field of molecular biology into what we know today. A must have, and an invaluable resource that will help the burgeoning, early scientist take one step closer to their future career of scientific independence and innovation.
Difficult to Understand and too much experimental data.......2005-05-15
I used this textbook for an undergraduate capstone class in molecular biology. The book is divided into eight main parts: Introduction, Methods in Molecular Biology, Transcription in Prokaryotes, Transcription in Eukaryotes, Posttranscriptional Events, Translation, and Genomes. The book is very detailed in its explanations of molecular processes and this makes it difficult to comprehend. Often, I would read a few pages and understand very little of what I read. I found that I learned more if I listened closely in class and only refered to the book for details, which is what I would suggest. Also my class focused mostly on problem based learning in molecular biology and less on memorizing molecular details. This book contains very few problems so my professor made up his own questions that he gave us and they were more helpful.
Another problem that I had with this book is that it contains probably too much experimental information. Almost every science textbook contains a little information about important discovers, but usually a little information is all that is needed. This book gives detailed descriptions of experiments that were used to discover principles of molecular biology, and I think that most and unnessary and only distract the student in what is already a confusing textbook. I understand that Dr. Weaver's aim was to introduce the experimental aspects of the subject, but I think he went a little overboard. Since this is an introductory textbook, primary principles should be focused on and specific experiments should be limited and should be found in side text-boxes instead of in the body of the text. That way, the student can read the experiments only if he or she is interested instead of having them interupt the subject matter at hand, which commonly occurs in the this textbook.
Regardless to say, I did not use this book to study from as much as I use most of my science books. Instead, I focused more on my professor's notes and questions and only referred to the book for key concepts. The book is not bad for key concepts and does contain and number of useful figures. Yet I would not recommend trying to read a chapter straight though; it is not worth it. Study the key ideas and figures instead. The remainder of the information is, in my opinion, a little advanced for an introductory class--although this book is intended for such a class--and way too wordy.
Average customer rating:
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Cytokine Reference: A Compendium of Cytokines and Other Mediators of Host Defense (Individual Version)
Manufacturer: Academic Press
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ASIN: 0122526708 |
Book Description
The Cytokine Reference is the most complete work for anyone interested in the role of cytokines in host defense processes. With essential and comprehensive information on all known cytokines, including chemokines, growth factors and neuropeptides, the database will include hundreds of entries with detailed descriptions of cytokine genes, proteins, cell sources, activities, receptors, receptor signal transduction, gene activation, pathophysiology, therapeutics and techniques. This encyclopedic reference is written by a panel of global experts and will include extensive tables and diagrams. This book/online bundle consists of a two-volume print set, plus a regularly updated and searchable Online Database.
Cytokines are produced by virtually all the cells in our bodies, and they regulate the systems that defend us against infection, tumors, and trauma. This publication and database will enable all those working in the field to find the information they need about this ever-expanding field.
* Online extensively-linked database is highly functional and allows you to reach data in a variety of ways--by cytokine, by cell type, or by disease
* Online version offers regularly updated entries and addition of new entries as research uncovers further information
* Print version has approximately 2500 pages of detailed and highly structured information on all the cytokines and other mediators of host defense
* Contains over 175 chapters contributed by international experts and edited by 6 world renowned scientists
* Online database allows extensive links at chapter subheading level guiding you through the maze of inter-relationships
* Online version includes full color diagrams and sequences plus links to online databases, including MEDLINE, PDB, SWISSPRO, and GenBank
* Every cytokine or receptor chapter uses the same highly structured subheadings, ensuring that the information is complete, comprehensive, and easy to find
Book Description
This new and expanded edition of the bestselling textbook has now been fully revised to include techniques from across the biosciences. It focuses particularly on those techniques that have led to recent advances in molecular biology and is designed to help students understand the theory and practical principles behind those methods. The book will be essential reading for all bioscience undergraduate students and pre-clinical medical students and will complement traditional undergraduate texts in biochemistry and molecular biology.
Customer Reviews:
good with an adjunct.......2005-04-14
this is a very nice book with abundant information.there are few topics which are dealt extraordinarily especially centrifugation,HPLC,electrophoresis etcetera.i have been studying this book from my graduation.initially i used to feel some difficulty with this book,so i studied biopysical and biophysical techniques by Upadhyaya and Upadhyaya.once i got the clear idea regarding the techniques,i shifted to this book.now i feel this book is very helpful.it is highly recommended to all biology students.
Excellent reference.......2003-05-09
This book is an invaluable source of information not only for those studying about various practical techniques but even those engaged in experiments in a lab environment. Written more as an overview, it works to familiarize the reader with the principles of both experimental protocols and the equipment that might be used, for example centrifuges. It's very useful to go back to it from time to time to get a refresher on techniques that I might use on a regular basis but might not remember all the details of. Highly recommended. It's also written quite simply, which unfortunately is not the case for all biology texts.
A useful, informative guide to practical biology.......1998-01-04
This book would be especially useful to science students engaging in a predominantly practical-based biological course.
Book Description
Published by New Science Press, this text introduces general principles of protein structure, folding, and function, then goes beyond these basics to tackle the conceptual basis of inferring structure and function from genomic sequence. It is the first book in a series, Primers in Biology, employing a modular design in which chapters are divided into topics, each occupying one two-page spread that includes the relevant text, illustrations (in full color), definitions, and references.
The book has five chapters. The first is an introduction to the principles of protein structure and folding, with emphasis on proteins' biophysical properties. The second describes the principles of the main biochemical functions of proteins, namely binding and catalysis, with a short section on the properties of structural proteins. Chapter 3 covers the regulation of protein function, containing concise descriptions of all the regulatory mechanisms that operate on proteins, from pH to phosphorylation, with several sections on protein switches based on nucleotide hydrolysis. Chapter 4 introduces the principles whereby structure and function are deduced from sequence, with illustrative examples. The final chapter addresses how data on protein structure is gathered, interpreted, and presented.
Written for upper-level undergraduates and beginning graduate students, Protein Structure and Function will also be useful for working scientists needing an up-to-date introduction to the field.
Customer Reviews:
Quality and content of the book........2006-02-25
Generally,the book is excellent and the information is condensed in a simple language which can be understood easily. I also liked the proteins cartoons, the protein data bank number,fantastic! In additions, the book have links,words or terms defination and further references which proves to be helpful.
To the point introduction .......2005-10-09
It is great! Concise, to the point, with good illustrations, teaches you the essentials of protein structure and function in little time.
Average customer rating:
- Outstanding introduction
- A long expected book in molecular modeling is finally here
- Beautifully written!
- Never short of something exciting
- Excellent book for both students and researchers
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Molecular Modeling and Simulation
Tamar Schlick
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ASIN: 038795404X |
Book Description
This book evolved from an interdisciplinary graduate course entitled Molecular Modeling developed at New York University. Its primary goal is to stimulate excitement for molecular modeling research while introducing readers to the wide range of biomolecular problems being solved by computational techniques and to those computational tools. The book is intended for beginning graduate students in medical schools and scientific fields such as biology, chemistry, physics, mathematics, and computer science. Other scientists who wish to enter, or become familiar, with the field of biomolecular modeling and simulation may also benefit from the broad coverage of problems and approaches. The book surveys three broad areas: biomolecular structure and modeling: current problems and state of computations; molecular mechanics: force field origin, composition, and evaluation techniques; and simulation methods: geometry optimization, Monte Carlo, and molecular dynamics approaches. Appendices featuring homework assignments, reading lists, and other information useful for teaching molecular modeling complement the material in the main text. Extensive use of world wide web resources is encouraged, and additional course and text information may be found on a supplementary website. Some praise for Tamar Schlick¿s ¿Molecular Modeling and Simulation: An Interdisciplinary Guide¿:||"The interdisciplinary structural biology community has waited long for a book of this kind which provides an excellent introduction to molecular modeling.¿|¿Harold A. Scheraga, Cornell University||"A uniquely valuable introduction to the modeling of biomolecular structure and dynamics. A rigorous and up-to-date treatment of the foundations, enlivened by engaging anecdotes and historical notes.¿|¿J. Andrew McCammon, Howard Hughes Medical Institute, University of California at San Diego||"I am often asked by physicists, mathematicians and engineers to recommend a book that would be useful to get them started in computational molecular biology. I am also often approached by my colleagues in computational biology to recommend a solid textbook for a graduate course in the area. Tamar Schlick has written the book that I will be recommending to both groups. Tamar has done an amazing job in writing a book that is both suitably accessible for beginners, and suitably rigorous for experts.¿|¿J.J. Collins, Boston University
Customer Reviews:
Outstanding introduction.......2004-05-13
... not only to molecular modeling, but to some of the subtleties of DNA and protein behavior and geometry, too.
This book's focus is generally on interactions with large molecules, DNA and proteins, although it does discuss small molecules (drugs, a few dozen to a few hundred atoms) too. That means that it skips most of the quantum mechanical modeling of more advanced computational chemistry texts.
Nothing is lost, because Schlick covers her chosen topic (molecular modeling and dynamics) in such detail. She starts with a very clear discussion of the structure of large biomolecules, with emphasis on the features that need quantitative description for modeling. That covers protein structure at ever level. It also covers DNA/RNA structure in the best detail I've ever seen. The double-helix is the just the starting point. There are alternative helix forms, non-standard binding between nucleotides, and asymmetries caused by nucleotide composition. The next chapters describe the geometric model and, briefly, the forces acting between atoms.
The second half of the book gets down to the nuts and bolts of modeling. This includes numerical techniques, minimization, sampling and Monte Carlo techniques, and the start of dynamics. Schlick attacks some of the nasty points of the calculations, such as modeling of forces that act on very different time scales. As with the simpler material, the development is clear, descriptive, and free of pointless theorems. The meticulous reader should come away able to implement most or all of the techniques described. The level of presentation is consistent and approachable. I think freshman physics should be enough preparation for most students to get most of the value out of the discussion.
The book is written with clarity as a top priority. The glossary is in the front, making sure that the reader knows it's a first-class part of the text. After that, every chapter starts with a list of the mathematical symbols and variables used and a one-line description of each. These are small things, but they increase the book's readability immensely. The illustrations are generally informative enough. On the whole, though, they don't seem quite up to the level of the textual and mathematical presentations.
I needed a crash course in the mathematical techniques used for describing molecular structure and behavior. I should have read this book first - its clarity and thoroughness would have saved me a lot of time. After this one, I can now go back and reread the more complex texts with more hops of understanding. Do yourself a favor and read this one first.
A long expected book in molecular modeling is finally here.......2004-02-17
I highly recommend Professor T. Schlick's book. It is beautifully written with many examples and great illustrations. The book is truly interdisciplinary; it covers, in good depth, both the biological and mathematical aspects of computational structural biology. Most chapters start with an amenable introduction and finish with "hands-on" recommendations and future challenges. I was particularly pleased with the level of detail in each chapter (in particular those that show the reader the advantages and pitfalls of the different methods presented). My colleague Mariel Vazquez and I used this book in the design and preparation of our "Special topics in Mathematics" course at the UC Berkeley Mathematics Department during the Spring of 2003.
This upper-level undergraduate/lower-level graduate course was centered on mathematical and computational models of the three dimensional structure of DNA, and DNA topology. We found Professor T. Schlick's book very useful in our class preparation. In particular we covered chapter 5 (DNA structure) completely, sections 3 and 4 from chapter 7 (basic principles and formulation of atomic interactions in molecular mechanics), and several sections or subsections from chapters 8 and 9 (force terms used in molecular dynamics simulations). We also covered most of the material in chapter 10 (Multivariate Minimization), and gave a brief introduction to chapter 11 (Monte-Carlo techniques) and chapter 12 (Molecular Dynamics algorithms).
Chapter 5 starts with a very amenable and brief introduction that relates DNA with other biological processes and describes some of the challenges in studying DNA structure. It continues describing the basic building blocks of DNA. The author wisely spends some time defining the nomenclature for each of the atoms, angles and bonds that form these basic blocks. The following sections teach the reader what parameters are relevant for describing a DNA double helix and how they characterize the A, B and Z- forms of DNA. Illustrations in this chapter are particularly helpful.
Although our course's approach to DNA supercoiling was different that the one in the book I found particularly useful some illustrations in chapter 6 and movies (to be found in her webpage) that Prof. Schlick's group has developed over the years. In brief, chapter 6 is a study of more complex structures and behavior of DNA (such as structural role of the DNA sequence, DNA-protein interactions, and higher order organization of DNA -i.e. DNA supercoiling and histone-DNA interactions). This chapter can be a good source for short research projects (e.g. final projects).
Chapters 7, 8 and 9 describe the basic concepts in molecular mechanics. From sections 7.3 and 7.4 I found of interest how the author addresses the problem of the system size (i.e. number of interacting molecules) and some of the details that the author gives for modeling the geometry of atomic interactions. At the end of the chapter (section 7.4.3) interested readers can find some of the limitations of current approaches. Chapters 8 and 9 describe in depth the force fields and how to implement them. Chapter 9 also illustrates with clarity how to implement periodic boundary conditions and the advantages of using different lattice models.
Chapter 10 describes a number of familiar methods for energy minimization (i.e. steepest descent, conjugate gradient, etc....). We used sections 10.1 to 10.4 and section 10.5.2 (conjugate gradient). I found the Hessian patterns shown in figures 10.4 and 10.5 and the minimization trajectories shown in 10.10 very pedagogical. As in previous chapters the author finishes with practical recommendations and future challenges.
We left chapter 11 (Monte Carlo methods) for last in the course and discussed chapter 12 (molecular dynamics) first. As in previous chapters the author gives a very nice introduction (section 12.1 and 12.2) and covers the basics on simulation protocols in sections 12.3 and 12.4. Section 12.4 describes the basic integration algorithms such as leap-frog, verlet, etc... Figure 12.3 was revealing for the students as it compares the time scales in biological systems.
Chapter 11 (Monte-Carlo methods) provides a very comprehensive introduction to Monte-Carlo methods. We found particularly useful some of the subsections of random number generation and the treatment of Importance sampling and Markov chains in section 11.5.
As mentioned earlier we were particularly delighted with the amount of details given in each topic. For example chapters 7 and 8 provide all the formalism needed for the problems of molecular mechanics. In section 8.4 (bond angle potential) the author highlights the differences (both formally and by figures-see figure 8.4) between different formulations of the problem (see also figure 8.6). In Chapter 10 the author describes minimization algorithms in detail and shows some of the patterns that one observes in the Hessian associated to minimization functions of biological structures (see figs. 10.4, 10.5 and 10.11). She also makes very detailed comparisons between the different minimization methods (see figs 10. 2, 10.10). In chapter 12 she compares the different methods and initial conditions for the algorithms discussed (figs 12.3, 12.4, 12.6).
Overall we found that Prof. T. Schlick's book is very adequate for a broad spectrum of levels and very accessible to both graduate and undergraduate students interested in mathematical modeling and computational biology. It is also very well organized facilitating the option of selecting parts of the material for the classroom or for use in one's research.
Beautifully written!.......2003-08-11
As a person with no expertise in molecular modeling who wanted to learn about this field, this book is right on! I find the author's lively text to be as well-written and clear as any science textbook I have ever read. I especially enjoyed the first two chapters for their historical perspective and their practical illustrations of applications of genetics in the world today. These chapters can be understood by non-scientists, whereas the rest of the book is clearly designed for graduate students in any one of the science disciplines.
The interesting information sprinkled throughout the book, including the boxes and figures, help keep the reader stimulated and yearning for greater knowledge of this exciting field. The color graphics also complement the book nicely. Although the subject covered in the book is extremely broad, the author managed to convey the perspectives of multiple scientific disciplines (e.g., biology, chemistry, computer science, math) very well. The combination of breadth and depth in a readable style is remarkable.
Overall, I highly recommend this book to readers interested in the area.
Never short of something exciting.......2003-08-11
It contains many many exiting problems and stimulate to go through the world of art of biology and mathematics. This book can guide the way where to go when you lost in the world of biomathematics, specifically molecular modeling. It looks like a well-organized dictionary with analysis. So it is good for a beginner and also deep-thinker in computational biology field.
Excellent book for both students and researchers.......2003-08-08
This book covers state-of-arts technologies used in today's hot field: molecular modeling. The book is easy to understand and it is suitable for graduate students in both theoretic majors and experimental majors. The homeworks in the book are practical for students to learn basic molecular modeling computer skills very fast.
Dr. Schlick is an expert in this field and her group has published tons of molecular modeling research papers. Her expertise also makes this book valuable for computational scientific researchers. I highly recommend it.
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