Table of Contents

Foreword.Preface.Acknowledgments.Contributors.SECTION I. INTRODUCTION.Defining Bioinformatics and Structural Bioinformatics (R. Altman & J. Dugan).Fundamentals of Protein Structure (E. Scheeff & L. Fink).Fundamentals of DNA and RNA Structure (S. Neidle, et al.).Computational Aspects of High-Throughput Crystallographic Macromolecular Structure Determination (P. Adams, et al.).Macromolecular Structure Determination by NMR Spectroscopy (J. Markley, et al.).Electron Microscopy (N. Volkmann & D. Hanein).Molecular Visualization (J. Tate).SECTION II. DATA REPRESENTATION AND DATABASES.The PDB Format, mmCIF Formats, and Other Data Formats (J. Westbrook & P. Fitzgerald).The Protein Data Bank (The PDB Team).The Nucleic Acid Database (H. Berman, et al.).Other Structure-Based Databases (H. Weissig & P. Bourne).SECTION III. COMPARATIVE FEATURES.Protein Structure Evolution and the SCOP Database (B. Reddy & P. Bourne). The CATH Domain Structure Database (C. Orengo, et al.).Structural Quality Assurance (R. Laskowski).All-Atom Contacts: A New Approach to Structure Validation (J. Richardson).Structure Comparison and Alignment (P. Bourne & I. Shinadyalov).SECTION IV. STRUCTURE AND FUNCTIONAL ASSIGNMENT.Secondary Structure Assignment (C. Andersen & B. Rost).Identifying Structural Domains in Proteins (L. Wernisch & S. Wodak).Inferring Protein Function from Structure (G. Bartlett, et al.).SECTION V. PROTEIN INTERACTIONS.Prediction of Protein-Protein Interactions from Evolutionary Information (A. Valencia & F. Pazos).Electrostatic Interactions (N. Baker & J. McCammon).SECTION VI. PROTEINS AS DRUG TARGETS.Principles and Methods of Docking and Ligand Design (J. Krumrine, et al.).Structural Bioinformatics in Drug Discovery (E. Fauman, et al.).SECTION VII. STRUCTURE PREDICTION.CASP and CAFASP Experiments and Their Findings (P. Bourne).Homology Modeling (E. Krieger, et al.).Fold Recognition Methods (A. Godzik).Ab Initio Methods (D. Chivian, et al.).Prediction in 1D: Secondary Structure, Membrane Helices, and Accessibility (B. Rost).SECTION VIII. THE FUTURE.Structural Genomics (S. Burley & J. Bonanno).Index.

About the Author

PHILIP E. BOURNE is a Professor in the Department of Pharmacology at the University of California San Diego and Director of Integrated Biosciences at the San Diego Supercomputer Center. He is also currently the President of the International Society for Computational Biology (ISCB). Dr. Bourne is the author of over 100 peer reviewed scientific papers and three previous books. HELGE WEISSIG is a Project Leader in Bioinformatics at ActivX Biosciences, a proteomics company, and also co-coordinates the Bioinformatics Certificate program for UCSD Extension. After doing his post-doctoral work with Prof. Bourne at the San Diego Supercomputer Center, he became the Technical Project Manager for the RCSB Protein Data Bank (PDB) at UCSD.

Reviews

"This book is a gold mine of fundamental and practical information in an area not previously well represented in book form." (Biochemistry and Molecular Education, September/October 2003) "...a gold mine of fundamental and practical information...This book is destined to become a classic reference work for workers at all levels in structural bioinformatics...recommended with great enthusiasm for educators, researchers, and graduate students." (BAMBED, Vol. 31, No. 5, 2003) "...recommended for anyone who wishes to develop bioinformatics tools for protein structure analysis." (The Biotech Journal, April/May 2003) "...a useful and timely summary of a rapidly expanding field." (Nature Structural Biology, Vol. 10, No. 8, August 2003) "...a terrific job in this timely creation of a compilation of articles that appropriately addresses this issue." (Briefings in Bioinformatics)