Molecular Modeling: Basic Principles and Applications

Book Description

Written by experienced experts in the field, this book describes the basics to the extent necessary for reliably judging the results from molecular modeling calculations.
Without unnecessary overhead, it leads readers from simple calculations on small molecules to the modeling of proteins and other relevant biomolecules. Beginners are guided through their first modeling experiment, while routine users of modeling software are provided with invaluable troubleshooting hints. A unique resource for students, researchers and lecturers, now available in this all-new, enlarged edition.

"If the currently popular 'Dummies' series of computer books were to publish a volume on molecular modeling this would be it" (Journal of the American Chemical Society)

"The book is well written and assumes no prior knowledge of molecular biology, statistical mechanics, or quantum chemistry. The authors provide practical hints for the application of the majority of available programs in computational chemistry" (Computers in Physics)

Customer Reviews:

Accelrys advertisement.......2007-01-17

This book describes what is essentially docking calculations in the context of the Accerlys software. The text is very qualitative and does not provide enough instruction to do any "molecular modeling". It seems to be more guidlines for various software packages sold by Accerlys.

Physical Biochemistry: Applications to Biochemistry and Molecular Biology

Average customer rating:

In bad need of an update

Physical Biochemistry: Applications to Biochemistry and Molecular Biology
David M. Freifelder
Manufacturer: W. H. Freeman
ProductGroup: Book
Binding: Paperback

Biochemistry | Biological Sciences | Science | Subjects | Books

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Natural History | Nature & Ecology | Science | Subjects | Books

Biochemistry | Basic Science | Medicine | Subjects | Books

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ASIN: 0716714442

Customer Reviews:

In bad need of an update.......2000-05-07

Now approaching an age of near 20, this book is in sore need of an updated edition. Never-the-less, Dr. Freifelder's classic on the techniques that biochemists use and must be facile with is still the most useful and informative book on this subject I've ever encountered. All of the techniques that were important at the time of the book's publication are extensively and clearly explained both from the theoretical and practical points of view. Unfortunately, some newer techniques introduced since that time are missing. Despite this, this book remains a must for graduate students in biochemistry and related disciplines.

Computer Simulation Of Biomolecular Systems: THEORETICAL AND EXPERIMENTAL APPLICATIONS VOL 3 (COMPUTER SIMULATION OF BIOMOLECULAR SYSTEMS)

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Computer Simulation Of Biomolecular Systems: THEORETICAL AND EXPERIMENTAL APPLICATIONS VOL 3 (COMPUTER SIMULATION OF BIOMOLECULAR SYSTEMS)
WILFRED F., ED. VAN GUNSTEREN
Manufacturer: Kluwer Academic Publishers
ProductGroup: Book
Binding: Hardcover

Modeling & Simulation | Computer Science | Computers & Internet | Subjects | Books

Biochemistry | Biological Sciences | Science | Subjects | Books

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ASIN: 9072199251

Book Description

This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress.
Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes.
The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in:

simulation methodology
the treatment of electrostatics
protein structure refinement
the combined experimental and theoretical approaches to the study of very large biological systems
applications and methodology involved in the study of protein folding
applications and methodology associated with structure-based design.

Free Energy Calculations: Theory and Applications in Chemistry and Biology (Springer Series in Chemical Physics)

Average customer rating:

A long-awaited reference

Free Energy Calculations: Theory and Applications in Chemistry and Biology (Springer Series in Chemical Physics)

Manufacturer: Springer
ProductGroup: Book
Binding: Paperback

General | Engineering | Professional & Technical | Subjects | Books

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Renewable Energy | Technology | Science | Subjects | Books

ASIN: 3540736174

Book Description

Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability.

This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles.

The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.

Customer Reviews:

A long-awaited reference.......2007-06-18

Free energy calculations have been around for several decades, and are now a field of their own, with its massive literature and a thick jungle of algorithms and implementations. Experienced researchers have to invest a lot of time to keep up to date (not everyone does), and to newcomers, it can be very confusing. Young researchers still use introductory material from the famous books of Allen and Tildesley, and Frenkel and Smit. While very precious, those are now old (especially Allen and Tildesley) and cover many other subjects, so they give little detail about classic techniques and virtually nothing about more recent ones, such as nonequilibrium methods or Wang-Landau sampling.

This book brings together a handful of recognized experts from around the globe, who try to sum up the state of the art in free energy calculations in a concise, yet in-depth manner. Newcomers to the field will appreciate the first chapter, which gives an overview and an introduction to essential concepts. The following chapters present the main families of methods in a systematic way, from transition path sampling to simplified methods designed to treat large biological systems efficiently. Depending on each author's style, the chapters have different balances of raw theory and real-world applications. Even authors writing mostly about theory try to keep an eye on practical implications. Beyond the formally exact equations, many chapters put an emphasis on finite sampling errors and methods to minimize them: in real life, that often makes the difference between free energy calculations that work and those that don't.

Spectroscopy of Inorganic Bioactivators: Theory and Applications - Chemistry, Physics, Biology, and Medicine (NATO Science Series C:)

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Spectroscopy of Inorganic Bioactivators: Theory and Applications - Chemistry, Physics, Biology, and Medicine (NATO Science Series C:)

Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

Biochemistry | Biological Sciences | Science | Subjects | Books

Crystallography | Chemistry | Science | Subjects | Books

General & Reference | Chemistry | Science | Subjects | Books

General | Science | Subjects | Books

Physiology | Basic Science | Medicine | Subjects | Books

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ASIN: 0792303016

Real-time Analysis Of Biomolecular Interactions: Applications of BIACORE

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Real-time Analysis Of Biomolecular Interactions: Applications of BIACORE
K., Ed. Nagata
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

Biochemistry | Biological Sciences | Science | Subjects | Books

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Book Description

The metabolism of all living organisms consists of elaborate and complex interactions among numbers of biomolecules, including protein-protein interactions. BIACORE is a new device that uses surface plasmon resonance for kinetic analysis of molecular interactions and automates whole analytical processes. The number of users of BIACORE is increasing worldwide, but until now nothing had been published in English to explain the principles of this new methodology and the kinds of applications it makes available. This updated and revised version of the Japanese original explains the underlying principles of BIACORE, providing concrete examples that utilize the methodology for analysis in areas ranging from basic to applied sciences. With its generous use of illustrations, this book is a valuable source of information for all users of BIACORE.

Average customer rating:

Watch the editions!!!

An absolutely beginner's guide to....

Excellent Introduction to Running!

A Good Resource for the Beginner

Pretty good

The Beginning Runner's Handbook: The Proven 13-Week Walk-Run Program
The Sports Medicine Council British Columbia
Manufacturer: Greystone Books
ProductGroup: Book
Binding: Paperback

Running & Jogging | Exercise & Fitness | Health, Mind & Body | Subjects | Books
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The Courage To Start: A Guide To Running for Your Life

No Need for Speed: A Beginner's Guide to the Joy of Running

The Runner's Handbook : The Bestselling Classic Fitness Guide for Beginning and Intermediate Runners (2nd rev Edition)

Runner's World Complete Book of Women's Running: The Best Advice to Get Started, Stay Motivated, Lose Weight, Run Injury-Free, Be Safe, and Train for Any Distance (Runner's World Complete Books)

The Beginning Runner's Journal: Based on the Walk/Run Program in the Bestselling Beginning Runner's Handbook

Accessories:

Tanita BC554 Ironman Glass InnerScan Body Composition Monitor Elite Series

ASIN: 1553650875

Book Description

At the core of this popular guide is "the program" — a 13-week walk/run plan designed to turn anyone into a runner, without injury. Originally developed by sports medicine physicians and refined through three years of clinics and responses from runners, it explains precisely how the beginner should train every day for the first 13 weeks. Every part of the process is covered, from equipment to staying motivated.

New to this edition are sections on training to run faster and farther, interval and tempo training; maintaining fitness on vacation; training for a half and full marathon; and coming back from injuries. A new chapter focuses on running and the family, including running during pregnancy and after the baby arrives, jogging strollers, children who want to run, and running with the family dog. Also included is the latest on nutrition and running, including low-carb diets and other popular diet trends.

Customer Reviews:

Watch the editions!!!.......2007-10-02

Just a note to those that are interested in buying this book. The 13-week run/walk program was completely revised between the 2001 and 2005 editions of the book. The 2001 edition is a much gentler approach, while the 2005 edition assumes that you have a certain level of fitness. Just to illustrate: the very first session of the first week of the 13 week program in the 2005 edition calls for "run 1 minute, walk 2 minutes; do this 12 times" (the 9th time just about killed me), whereas the 2001 edition of the book starts with "run 30 seconds, walk 4 minutes 30 seconds; do this 7 times". So if you're more fit you may be happy with the 2005 edition, otherwise try to find the 2001 or 1999 editions of the book. Otherwise, I liked the book a lot.

An absolutely beginner's guide to...........2007-09-14

...Running! This is a very decent introduction (and also highly motivational) for someone very new to running. In my humble opinion, this is not a book for even someone that is slightly advanced into running. If you are someone that has been into a program and can run 5Ks and want to improve your time or improve breathing skills, this is not the book for you. However, if you are just beginning to run (and want to motivate yourself), then this is a good book. That is the reason why I gave the book 4 stars because it says it is a beginner's runner book. I just assumed that I would find tips such as rythmic breathing or other skills that will help you run better. good luck and keep running because its good for you!

Excellent Introduction to Running!.......2007-09-09

I bought this book two years ago (the 2005 edition) and it gave me the basis I needed to keep running ever since. The book lives up to its title and gives you a practical program for running 60+ minutes by the end, gradually helping you break yourself into it.

I'm puzzled by some of the negative reviews here because it is very much geared for people who have never run or haven't done so in so long they don't know how to begin again. It covers all the basics you'll need to know about stretching, nutrition, injury avoidance and treatment, goal setting, clothing, and crosstraining, and it explains how these are important in relation to your running. It even gives tips on issues like running while pregnant, with a stroller, or how to get your kids involved if you want to try and make running a family affair.

The program itself is great, and while I was always pushing myself (and was even intimidated sometimes looking at what I had to do for my next run), it was never more than I could handle. I found I was so unprepared for running that I had to take an extra "pre-training" week in which I halved the first week's goals, but after that there was never a problem. Additionally, one of my favorite things about the book besides the program is all the little synopses of interviews with different runners that give you a sense of just how diverse they are - young/old, heavy/lean, competitive/recreational - as well as the reasons why they run. You're bound to find yourself identifing with (and being inspired by) some of them!

When I started this program almost two years ago, a minute of running left me winded and beat. Tomorrow I'm running ten miles in preparation for a half-marathon at the end of next month. All told, I'd say it definitely works and I wholeheartedly recommend it!

A Good Resource for the Beginner.......2007-05-20

In November 2006 I bought 2 books, The Beginning Runner's Handbook by Ian MacNeill, and The Courage to Start by John Bingham. These books changed my life. I was an athlete when I was younger (I played rugby in high school and college, threw the discus and shot put, practiced martial arts, and played competitive softball) and running was always a necessary evil of being part of a sports team. I hated it. I never thought that I would run just to run, and like it. The MacNeill book has a 13-week run-walk plan to go from a coach potato to being able to run a 10k, starting with a lot of walking and working toward mostly running. After the initial 13 weeks, it also has more advanced training plans to maintain your level of fitness, and plans to increase speed, and increase distance. They suggest adding distance very slowly, a little each week (like 10%) to minimize the chances of getting hurt.

When I started I weighed around 300 pounds. Then I started running and eating more sensibly. I've lost 54 pounds, with the hope of getting to my playing weight, which was in the 210-220 range. I am running 3-6 miles three times a week, and hope to be able to build up to more. If I can do this, anyone can. Good luck!

Pretty good.......2007-05-12

The plans at the back of the book alone are worth buying this book. It's truly catered to the ultimate beginner. It even has a 13 week walk program for those not physically ready to stress their body with jogging yet. I'm not much of an athlete but several years ago I had managed to train hard and learn to run for some training that my job requires. Then, I had knee surgery and decided to sit on the couch too long afterwards! I'm on week 8 of this program and back in the swing of things just fine. I've repeated 2 of the weeks just to give myself time to really build my endurance again- repeating weeks is suggested in the book if you think you need it. The only caution I will put on this book is that it's long on motivational stories and quotes that I just didn't need. I wish it had focused more on health, nutrition, physiology of running and injuries.

The Beginning Runner's Handbook: The Proven 13-Week Walk/Run Program

Average customer rating:

The Beginning Runner's Handbook: The Proven 13-Week Walk/Run Program
Ian Macneill
Manufacturer: Greystone Books
ProductGroup: Book
Binding: Paperback
ASIN: B000PDVF5G

Book Description

This is the most complete guide to Oregon available. From accommodations to entertainment, it provides tons of options and tips for all travelers. Visit Coos Bay and the Columbia River Gorge, explore Kentucky Falls and the Twilight Eagle Sanctuary, and read about Civil War connections and geological anomalies. This updated edition has more information on Portland, new chapters on historical events, and information on the only lift-serviced summer skiing in the country. "Comprehensive, readable guide, with 120 pages devoted to the coast." -- Travel & Leisure

Customer Reviews:

Good Primer Before Going.......2003-12-06

I purchased and fully read the book for the purpose of preparing me for a recent two week trip to look over Oregon before a possible move there. The authors provide good quantity and quality of information about everything from history to permits to make-up of modern Oregon. If a reader purchased this book as his overall primer prior to travelling Oregon, he would do well. If one is interested in specific activities such as camping or fishing, there are better books. My only criticism is that although needed information is pretty much in this book, I had to do a lot of reading to get it rather than be able to look at the table of contents and pick my subjects. I would have liked, for example, a section just on camping and an explanation of free facilities like most state parks and about the permits required and where attainable for federal forests and other areas. The information is in the book; you just have to dig for it a bit. Overall, I am glad I purchased this book.

Oregon Handbook.......2002-08-07

As general reading this book is OK but I felt that it really missed the mark in its attempt to be a guide to Oregon. There seem to be a lot of holes in it. Also items that are listed in the index are not where they are supposed to be.

A good guidebook by well-fed authors.......2000-08-11

This guide offers Moon's usual comprehensive treatment of local histories and sightseeing details. Despite some awkward English, it is generally reliable and reasonably complete.

After some perusing it becomes clear what is a major interest, even passion, of the authors and apparently a subject of extensive research by them - food. In every town, ample attention is given to restaurants, listing appetizers, main courses, desserts, even ingredients. . . three pages on Bend are devoted to eating, as are 11 pages in the Portland section. There are also two pages of reviews of golf courses that are replacing mountain meadows in the Bend area.

Unfortunately, the space devoted to food reduces what can be covered regarding another Moon staple - nature. In the Bend area, there's no detail on where to go hiking in the Three Sisters Wilderness. On Crater Lake, there's no park map and only two of a dozen trails are described.

The detail on what to see in many localities makes this book a worthwhile purchase for anybody planning a visit. But if you are as into nature as many readers of Moon guidebooks, expect to supplement the book with National Forest maps and a good local hiking guide.

Customer Reviews:

I found this book in a discount store.......2004-04-20

(...)The book is amazing. Secrets, violence, love all wound into one book great for teens and adults alike. What disappointed me most about this book, was that when I read it 2 years ago, I found that it was not in print any more! I am glad it is back again. No one should miss out on any book.

Completely wonderful.......2003-08-17

I found this book in a discount bin and can't for the life of me figure out why. This is one of the most timely and relevant books for urban children that I can think of. This book deals with issues of teen violence, death and family.

Would you hide a gun because a family member asked you to? Is it disloyal to your family not to hide it? What if you knew that your cousin had a gun and thought it was his ticket out of the nowhere oppression of a dead end town? Would you tell? Would you tell when his best friend ends up dead because of the gun?

This story of an African-American girl trying to decide where the bonds of family loyalty lie is one of the best I've ever seen. Her father dumps her at her Auntie's house each summer, even though he acts for all the world as if he is ashamed of where he came from now that he is a rich lawyer in New York. Her cousin wants out of this town and a life of priviledge in New York, just like her father. But does he understand that it took college and hard work to get there or does he think the Raven handgun he has hidden in her dollhouse is his ticket the easy way? Should she tell her Aunt that it is there?

For all the darkness of this book, it has an affirming, loving ending. The bonds and love of family pull close around this little girl, her troubled cousin and her father. The lesson learned here is that family and love, if trusted, will prevail.

Average customer rating:
RAVEN IN A DOVE HOUSE
DAVIS PINKEY ANDREA
Manufacturer: GULLIVER BOOKS/HARCOURT BRACE
ProductGroup: Book
Binding: Hardcover
ASIN: B000PGGAB2

Average customer rating:
Raven in a Dove House
Andrea Davis Pinkney
Manufacturer: Gulliver Books
ProductGroup: Book
Binding: Paperback
ASIN: B000OJL85S

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