Computational biochemistry and biophysics 2001
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Computational biochemistry and biophysics 2001
COMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 ok is printed on acid-free paper.HeadquartersMarcel Dekker. Inc.270 Madison Avenue. New York. NY 10016tel: 212-696-9000: fax: 212-685-4540Eastern Hemisphere DistributionMarcel Dekker AGHutgasse 4. Postfach 812. CH-4001 Basel. Switzerlandtel: 41-61-261-8482: fax: 41-61-261-8896World Wide Webhttp://ww Computational biochemistry and biophysics 2001 w.dekker.comThe publisher offers discounts on this book when ordered in bulk quantities. For more information, write to Special Sales/Professional MarComputational biochemistry and biophysics 2001
keting at the headquarters address above.Copyright © 2001 by Marcel Dekker. Inc. All Rights Reserved.Neither this book nor any part may be reproduced COMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 ge and retrieval system, without permission in writing from the publisher.Current printing (last digit):10 9 8 7 6 5 4 3 2 IForewordThe long-range goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last 70 years great progress has been m Computational biochemistry and biophysics 2001 ade in applying the quantum mechanical equations representing the underlying physical laws to chemical problems involving the structures and reactionsComputational biochemistry and biophysics 2001
of small molecules. This work was recognized in the awarding of the Nobel Prize in Chemistry to Walter Kohn and John Pople in 1998. Computational stuCOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 roperties of these systems, and the molecular dynamics simulation method is the most important theoretical approach used in such studies. The first molecular dynamics simulation of a protein, the bovine pancreatic trypsin inhibitor (BPT1), was published more than 20 years ago [I]. Although the simul Computational biochemistry and biophysics 2001 ation was *‘crude*’ by present standards, it was important because it introduced an important conceptual change in our view of biomolecules. The classComputational biochemistry and biophysics 2001
ic view of biopolymers, like proteins and nucleic acids, had been static in character. The remarkable detail evident in the protein crystal structuresCOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 rumental in changing the static view of the structure of biomolecules to a dynamic picture. It is now recognized that the atoms of w hich biopolymers are composed are in a state of constant motion at ordinary temperatures. The X-ray structure of a protein provides the average atomic positions, but t Computational biochemistry and biophysics 2001 he atoms exhibit fluidlike motions of sizable amplitudes about these averages. The new understanding of protein dynamics subsumed the static picture iComputational biochemistry and biophysics 2001
n that the average positions are still useful for the discussion of many aspects of biomolecule function in the language of structural chemistry. The COMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 vening years, molecular dynamics simulations of biomolecules have undergone an explosive development and been applied to a wide range of problems [3.4]. Two attributes of molecular dynamics simulations have played an essential role in their increasing use. The first is that simulations provide indiv Computational biochemistry and biophysics 2001 idual panicle motions as a function of time so they can answer detailed questions about the properties of a system, often more easily than experimentsComputational biochemistry and biophysics 2001
. For manv aspects of biomolecule function, it is these detailsivForewordthat are of interest (e.g.. by what pathways does oxygen get into and exit thCOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 the potential used in the simulations is approximate, it is completely under the user's control, so that by removing or altering specific contributions to the potential, their role in determining a given property can be examined. This is most graphically demonstrated in the calculation of free energ Computational biochemistry and biophysics 2001 y differences by “computer alchemy” in which the potential is transmuted reversibly from that representing one system to another during a simulation [Computational biochemistry and biophysics 2001
5].There are three types of applications of molecular dynamics simulation methods in the study of macromolecules of biological interest, as in other aCOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 f molecular dynamics, often with simulated annealing protocols, to determine or refine structures w ith data obtained from experiments, such as X-ray diffraction. The second uses simulations to determine equilibrium averages, including structural and motional properties (e.g., atomic mean-square flu Computational biochemistry and biophysics 2001 ctuation amplitudes) and the thermodynamics of the system. For such applications, it is necessary that the simulations adequately sample configurationComputational biochemistry and biophysics 2001
space, as in the first application, with the additional condition that each point be weighted by the appropriate Boltzmann factor. The third area empCOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 ed, but it must be done so as to properly represent the time development of the system. For the first two areas. Monte Carlo simulations, as well as molecular dynamics, can be utilized. By contrast, in the third area w here the motions and their development are of interest, only molecular dynamics c Computational biochemistry and biophysics 2001 an provide the necessary information. The three types of applications. all of which are considered in the present volume, make increasing demands on tComputational biochemistry and biophysics 2001
he simulation methodology in terms of the accuracy that is required.In the early years of molecular dynamics simulations of biomolecules, almost all sCOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 of the power and limitations of the approach. Now that the methodology is becoming more accessible (in terms of ease of application of generally distributed programs and the availability of the required computational resources) and better validated (in terms of published results), many people are b Computational biochemistry and biophysics 2001 eginning to use simulation technology without training in the area. Molecular dynamics simulations are becoming part of the ’“tool kit” used by everyoComputational biochemistry and biophysics 2001
ne, even experimentalists. who wish to obtain an understanding of the structure and function of biomolecules. To be able to do this effectively, a perCOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 s volume has an important role to play in the transition of the field from one limited to specialists (although they will continue to be needed to improve the methodology and extend its applicability) to the mainstream of molecular biology. The emphasis on an in-depth description of the computationa Computational biochemistry and biophysics 2001 l methodology will make the volume useful as an introduction to the field for many people who are doing simulations for the first time. They w ill finComputational biochemistry and biophysics 2001
d it helpful also to look at two earlier volumes on macromolecular simulations [3.4], as well as the classic general text on molecular dynamics [6]. ECOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 ular dynamics simulations are playing an essential role. A number of well-chosen ‘‘special topics” in-ForewordVthe perspective of the book by introducing approaches other than molecular dynamics for modeling proteins and their interactions. They make the connection with what many people regard—mista Computational biochemistry and biophysics 2001 kenly, in my view—as “computational biology/’ Certainly with the announced completion of a description of the human genome in a coarse-grained sense,Computational biochemistry and biophysics 2001
the part of computational biology concerned with the prediction of the structure and function of gene products from a knowledge of the polypeptide seqCOMPUTATIONAL BIOCHEMISTRY AND BIOPHYSICSedited by Oren M. Becker Alexander D. MacKerell, Jr.Benoit Roux Masakatsu WatanabeISBN: 0-8247-0455-XThis boo Computational biochemistry and biophysics 2001 The first set of Investigators in Computational Biology chosen this year demonstrates that the Howard Hughes Foundation recognized the importance of such biophysical studies to which this volume serves as an excellent introduction.I am very pleased to have been given the opportunity to contribute a Computational biochemistry and biophysics 2001 Foreword to this very useful book. It is a particular pleasure for me to do so because all the editors and fifteen of the authors are alumni of my resComputational biochemistry and biophysics 2001
earch group at Harvard, where molecular dynamics simulations of biomolecules originated.REFERENCES1.JA McCammon. BR Gelin. and M Karplus. Nature 267:5Gọi ngay
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