Computational Methods for Protein Structure Prediction & Modeling V1 - Xu Xu and Liang.pdf - ksiazki w pdf - shaerogorath

BIOLOGICAL AND MEDICAL PHYSICS,

BIOMEDICAL ENGINEERING

BIOLOGICAL AND MEDICAL PHYSICS

BIOMEDICAL ENGINEERING

Editor-in-Chief:

Elias Greenbaum, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

Volumes Published in This Series:

The Physics of Cerebrovascular Diseases, Hademenos, G.J., and Massoud, T.F., 1997

Lipid Bilayers: Structure and Interactions, Katsaras, J., 1999

Physics with Illustrative Examples from Medicine and Biology: Mechanics, Second Edition,

Benedek, G.B., and Villars, F.M.H., 2000

Physics with Illustrative Examples from Medicine and Biology: Statistical Physics, Second

Edition, Benedek, G.B., and Villars, F.M.H., 2000

Physics with Illustrative Examples from Medicine and Biology: Electricity and Magnetism,

Second Edition, Benedek, G.B., and Villars, F.M.H., 2000

Physics of Pulsatile Flow, Zamir, M., 2000

Molecular Engineering of Nanosystems, Rietman, E.A., 2001

Biological Systems Under Extreme Conditions: Structure and Function, Taniguchi, Y. et al., 2001

Intermediate Physics for Medicine and Biology, Third Edition, Hobbie, R.K., 2001

Epilepsy as a Dynamic Disease, Milton, J., and Jung, P. (Eds), 2002

Photonics of Biopolymers, Vekshin, N.L., 2002

Photocatalysis: Science and Technology, Kaneko, M., and Okura, I., 2002

E. coli in Motion, Berg, H.C., 2004

Biochips: Technology and Applications, Xing, W.-L., and Cheng, J. (Eds.), 2003

Laser-Tissue Interactions: Fundamentals and Applications, Niemz, M., 2003

Medical Applications of Nuclear Physics, Bethge, K., 2004

Biological Imaging and Sensing, Furukawa, T. (Ed.), 2004

Biomaterials and Tissue Engineering, Shi, D., 2004

Biomedical Devices and Their Applications, Shi, D., 2004

Microarray Technology and Its Applications, Muller, U.R., and Nicolau, D.V. (Eds), 2004

Emergent Computation: Emphasizing Bioinformatics, Simon, M., 2005

Molecular and Cellular Signaling, Beckerman, M., March 22, 2005

The Physics of Coronary Blood Flow, Zamir, M., May, 2005

The Physics of Birdsong Mindlin, G.B., Laje, R., August, 2005

Radiation Physics for Medical Physicists Podgorsak, E.B., September 2005

Neutron Scattering in Biology—Techniques and Applications Fitter, J., Gutberlet, T., Katsaras, J.

(Eds.), January 2006

Forthcoming Titles

Topology in Molecular Biology: DNA and Proteins Monastyrsky, M.I. (Ed.), 2006

Optical Polarization in Biomedical Applications Tuchin, V.V., Wang, L. (et al.), 2006

Continued After Index

Ying Xu, Dong Xu, and

Jie Liang (Eds.)

Computational Methods

for Protein Structure

Prediction and Modeling

Volume 1: Basic Characterization

Ying Xu

Department of Biochemistry

and Molecular Biology

University of Georgia

120 Green Street

Athens, GA 30602

USA

email: xyn@bmb.uga.edu

Dong Xu

Department of Computer Science

Digital Biology Laboratory

University of Missouri–Columbia

201 Engineering Building West

Columbia, MO 65211

USA

email: xudong@missouri.edu

Jie Liang

Department of Bioengineering

Center for Bioinformatics

University of Illinois at Chicago

851 S. Morgan Street

Chicago, IL 60607

USA

email: jliang@uic.edu

Library of Congress Control Number: 2006929615

ISBN 10: 0-387-33319-3

ISBN 13: 978-0387-33319-9

Printed on acid-free paper.

2007 Springer Science+Business Media, LLC

of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for

brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information

storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now

known or hereafter developed is forbidden.

The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are

not identiﬁed as such, is not to be taken as an expression of opinion as to whether or not they are subject to

proprietary rights.

987654321

springer.com

Preface

An ultimate goal of modern biology is to understand how the genetic blueprint of

cells (genotype) determines the structure, function, and behavior of a living organism

(phenotype). At the center of this scientiﬁc endeavor is characterizing the biochem-

ical and cellular roles of proteins, the working molecules of the machinery of life. A

key to understanding of functional proteins is the knowledge of their folded struc-

tures in a cell, as the structures provide the basis for studying proteins’ functions

and functional mechanisms at the molecular level.

Researchers working on structure determination have traditionally selected in-

dividual proteins due to their functional importance in a biological process or path-

way of particular interest. Major research organizations often have their own protein

X-ray crystallographic or/and nuclear magnetic resonance facilities for structure de-

termination, which have been conducted at a rate of a few to dozens of structures a

year. Realizing the widening gap between the rates of protein identiﬁcation (through

DNA sequencing and identiﬁcation of potential genes through bioinformatics anal-

ysis) and the determination of protein structures, a number of large scientiﬁc initia-

tives have been launched in the past few years by government funding agencies in

the United States, Europe, and Japan, with the intention to solve protein structures

en masse, an effort called structural genomics . A number of structural genomics

centers (factory-like facilities) have been established that promise to produce solved

protein structures in a similar fashion to DNA sequencing. These efforts as well as

the growth in the size of the community and the substantive increases in the ease

of structure determination, powered with a new generation of technologies such as

synchrotron radiation sources and high-resolution NMR, have accelerated the rate

of protein structure determination over the past decade. As of January 2006, the

protein structure database PDB contained

∼

34,500 protein structures.

The role of structure for biological sciences and research has grown consider-

ably since the advent of systems biology and the increased emphasis on understand-

ing molecular mechanisms from basic biology to clinical medicine. Just as every

geneticist or cell biologist needed in the 1990s to obtain the sequence of the gene

whose product or function they were studying, increasingly, those biologists will

need to know the structure of the gene product for their research programs in this

century. One can anticipate that the rate of structure determination will continue to

grow. However, the large expenses and technical details of structure determination

mean that it will remain difﬁcult to obtain experimental structures for more than a

small fraction of the proteins of interest to biologists. In contrast, DNA sequence

determination has doubled routinely in output for a couple of decades. The genome

projects have led to the production of 100 gigabytes of DNA data in Genbank, and

Computational Methods for Protein Structure Prediction & Modeling V1 - Xu Xu and Liang.pdf

Plik z chomika:

Inne pliki z tego folderu:

Inne foldery tego chomika: